NAMD-L: By Thread

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NAMD-L: By Thread

By Thread

1614 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Fri Jan 03 2020 - 07:25:25 CST
Ending: Thu Dec 30 2021 - 09:20:14 CST

Angle parameter errors Pradeepti Kampani (Thu Dec 30 2021 - 03:26:26 CST)
- Re: Angle parameter errors Vermaas, Josh (Thu Dec 30 2021 - 09:20:02 CST)
membrane system displacing in z during ABF or metadynamics Yogesh Sharma (Tue Dec 28 2021 - 04:58:26 CST)
- Re: membrane system displacing in z during ABF or metadynamics Josh Vermaas (Tue Dec 28 2021 - 07:46:56 CST)
simulation of protein DNA complex Dhiraj Srivastava (Mon Dec 27 2021 - 19:33:47 CST)
Re: namd-l digest V1 #3189 Raman Preet Singh (Mon Dec 27 2021 - 07:08:59 CST)
SMD at constant velocity Almeida-Hernández, Yasser, Dr. (Mon Dec 27 2021 - 04:45:32 CST)
- Re: SMD at constant velocity Giacomo Fiorin (Mon Dec 27 2021 - 10:14:57 CST)
  - Re: SMD at constant velocity Almeida-Hernández, Yasser, Dr. (Tue Dec 28 2021 - 04:45:00 CST)
    - Re: SMD at constant velocity Giacomo Fiorin (Tue Dec 28 2021 - 10:06:14 CST)
Question about CHARMM-GUI NAMD Inputs Ahmad Alqaisi (Sun Dec 26 2021 - 18:41:30 CST)
- Re: Question about CHARMM-GUI NAMD Inputs Vermaas, Josh (Mon Dec 27 2021 - 09:39:13 CST)
Position restrain in ABF Yogesh Sharma (Thu Dec 23 2021 - 07:36:28 CST)
Best performance multi node GPU Luis Cebamanos (Thu Dec 16 2021 - 09:05:56 CST)
- How to run on multi-node environment Luis Cebamanos (Wed Dec 22 2021 - 08:39:58 CST)
  - Re: How to run on multi-node environment Vermaas, Josh (Wed Dec 22 2021 - 08:56:03 CST)
tclForce not recognizing group option during cphmd job Diship Srivastava (Wed Dec 15 2021 - 23:42:58 CST)
Lone pair forces Hsubo Luo (Wed Dec 15 2021 - 11:15:40 CST)
SMD: Fixing centroid Moumita Saharay (Tue Dec 14 2021 - 04:18:10 CST)
- Re: SMD: Fixing centroid Anup Prasad (Tue Dec 14 2021 - 05:02:53 CST)
  - Re: SMD: Fixing centroid JÃ©rÃ´me HÃ©nin (Tue Dec 14 2021 - 08:10:25 CST)
    - Re: SMD: Fixing centroid Almeida-Hernández, Yasser, Dr. (Mon Dec 20 2021 - 07:00:55 CST)
    - Re: SMD: Fixing centroid ROPÃ“N-PALACIOS G. (Mon Dec 20 2021 - 12:17:48 CST)
(no subject) Rakesh Roy (Mon Dec 13 2021 - 07:19:12 CST)
Initial force for steered MD simulations Hannah Scott (Thu Dec 09 2021 - 14:42:28 CST)
- Re: Initial force for steered MD simulations ROPÃ“N-PALACIOS G. (Thu Dec 09 2021 - 18:43:38 CST)
  - Re: Initial force for steered MD simulations Hannah Scott (Mon Dec 27 2021 - 09:46:23 CST)
Problem with titration curve with cphanalyze script CYS and LYS (Constant pH Molecular Dynamics ) Ingrid Bernardes Santana Martins (Thu Dec 09 2021 - 07:00:17 CST)
- Re: Problem with titration curve with cphanalyze script CYS and LYS (Constant pH Molecular Dynamics ) Brian Radak (Fri Dec 10 2021 - 12:28:39 CST)
  - Re: Problem with titration curve with cphanalyze script CYS and LYS (Constant pH Molecular Dynamics ) Brian Radak (Fri Dec 10 2021 - 16:01:10 CST)
Error in running multiple-walkers metadynamics at Bluewaters Chen, Charles (Wed Dec 08 2021 - 18:29:27 CST)
- Re: Error in running multiple-walkers metadynamics at Bluewaters Giacomo Fiorin (Wed Dec 08 2021 - 19:12:09 CST)
restarting eABF jobs Ashutosh Shandilya (Wed Dec 08 2021 - 16:50:03 CST)
- Re: restarting eABF jobs Giacomo Fiorin (Wed Dec 08 2021 - 16:56:29 CST)
  - Re: restarting eABF jobs Ashutosh Shandilya (Wed Dec 08 2021 - 17:16:35 CST)
    - Re: restarting eABF jobs Ashutosh Shandilya (Wed Dec 08 2021 - 17:19:15 CST)
    - Re: restarting eABF jobs Giacomo Fiorin (Wed Dec 08 2021 - 19:05:58 CST)
Namd can not find parameters for chlorine lonepairs DENILSON FERREIRA DE OLIVEIRA (Wed Dec 08 2021 - 07:38:24 CST)
- Re: Namd can not find parameters for chlorine lonepairs Michael Robinson (Wed Dec 08 2021 - 18:26:27 CST)
Extracting force on subset of atoms from tclForces Nate Walkins (Tue Dec 07 2021 - 04:07:11 CST)
Dihedral parameters for terminal alkyne DENILSON FERREIRA DE OLIVEIRA (Sun Dec 05 2021 - 12:53:41 CST)
- Re: Dihedral parameters for terminal alkyne Fabrice Gardebien (Sun Dec 05 2021 - 23:35:07 CST)
  - Re: Dihedral parameters for terminal alkyne DENILSON FERREIRA DE OLIVEIRA (Sun Dec 12 2021 - 13:53:40 CST)
- Re: Dihedral parameters for terminal alkyne Michael Robinson (Mon Dec 06 2021 - 05:45:42 CST)
  - Re: Dihedral parameters for terminal alkyne DENILSON FERREIRA DE OLIVEIRA (Wed Dec 08 2021 - 07:06:18 CST)
eFieldNormalized Fateme Ghadirian (Sat Dec 04 2021 - 07:56:47 CST)
- Re: eFieldNormalized Giacomo Fiorin (Sat Dec 04 2021 - 14:09:38 CST)
  - Re: eFieldNormalized Hemanth Haridas (Sat Dec 04 2021 - 21:24:25 CST)
    - Re: eFieldNormalized Fateme Ghadirian (Sun Dec 05 2021 - 09:32:22 CST)
  - Re: eFieldNormalized Fateme Ghadirian (Sun Dec 05 2021 - 09:29:36 CST)
setting the value of qmLinkElement in NAMD/QMMM script jing liang (Thu Dec 02 2021 - 03:23:24 CST)
- Re: setting the value of qmLinkElement in NAMD/QMMM script Marcelo C. R. Melo (Thu Dec 02 2021 - 11:05:25 CST)
NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Vlad Cojocaru (Tue Nov 30 2021 - 04:30:35 CST)
- Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Axel Kohlmeyer (Tue Nov 30 2021 - 05:14:31 CST)
  - Re: NAMD performance on a supercomputer with Intel Xeon Platinum 8160 and 100Gb Intel Omni-Path Full-Fat Tree Giacomo Fiorin (Tue Nov 30 2021 - 08:33:18 CST)
FEP calculation for Binding of a potassium ion to 18Q=80=93crown=E2=80=936?= SYEDA SABIHA SULTANA LUBNA . (Thu Nov 25 2021 - 04:14:03 CST)
residue_rmsd.tcl script Alexei Rossokhin (Thu Nov 25 2021 - 02:15:39 CST)
- Re: residue_rmsd.tcl script Peter Freddolino (Thu Nov 25 2021 - 10:47:29 CST)
  - Re: residue_rmsd.tcl script Alexei Rossokhin (Fri Nov 26 2021 - 01:36:07 CST)
QMMM convergence/optimization issues in CHCL3 solvent Francesco Pietra (Tue Nov 23 2021 - 10:26:50 CST)
- Fwd: QMMM convergence/optimization issues in CHCL3 solvent Francesco Pietra (Tue Nov 23 2021 - 10:43:26 CST)
- Re: QMMM convergence/optimization issues in CHCL3 solvent Mariano Spivak (Tue Nov 23 2021 - 10:47:07 CST)
  - Re: QMMM convergence/optimization issues in CHCL3 solvent Francesco Pietra (Tue Nov 23 2021 - 14:32:04 CST)
HarmonicWall colvar ROPÃ“N-PALACIOS G. (Mon Nov 22 2021 - 12:25:57 CST)
- Re: HarmonicWall colvar JÃ©rÃ´me HÃ©nin (Tue Nov 23 2021 - 09:21:14 CST)
eFieldNormalized Fateme Ghadirian (Sat Nov 20 2021 - 10:26:31 CST)
applying harmonic constraints in cphmd Diship Srivastava (Fri Nov 19 2021 - 23:29:34 CST)
- Re: applying harmonic constraints in cphmd Brian Radak (Sat Nov 20 2021 - 10:25:31 CST)
  - Re: applying harmonic constraints in cphmd Diship Srivastava (Mon Nov 22 2021 - 03:58:09 CST)
    - Re: applying harmonic constraints in cphmd Brian Radak (Mon Nov 22 2021 - 13:05:40 CST)
colvars.traj file empty Ashutosh Shandilya (Thu Nov 18 2021 - 19:40:50 CST)
- Re: colvars.traj file empty Giacomo Fiorin (Thu Nov 18 2021 - 21:05:07 CST)
namd minimization looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 02:27:31 CST)
- Re: namd minimization looking for wrong angle Francesco Pietra (Thu Nov 18 2021 - 04:02:10 CST)
  - Re: namd minimization looking for wrong angle Peter Freddolino (Thu Nov 18 2021 - 08:03:40 CST)
colvars: Too many iterations in routine jacobi. Ashutosh Shandilya (Wed Nov 17 2021 - 09:58:33 CST)
- Re: colvars: Too many iterations in routine jacobi. Giacomo Fiorin (Wed Nov 17 2021 - 10:27:39 CST)
  - Re: colvars: Too many iterations in routine jacobi. Ashutosh Shandilya (Wed Nov 17 2021 - 11:51:32 CST)
User defined signal 2 ERROR: One or more process (first noticed rank 7) terminated with signal 12 Ashutosh Shandilya (Wed Nov 17 2021 - 09:09:07 CST)
QMMM latency in PME correction Wall, Michael E (Tue Nov 16 2021 - 15:39:25 CST)
- Re: QMMM latency in PME correction Marcelo C. R. Melo (Wed Nov 17 2021 - 21:01:19 CST)
Gallium parameters ROPÃ“N-PALACIOS G. (Tue Nov 16 2021 - 11:25:32 CST)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 è¾›å¿—å®� (Fri Nov 12 2021 - 08:35:40 CST)
- Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 Josh Vermaas (Fri Nov 12 2021 - 08:59:35 CST)
  - Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 Kushal Raj Roy (Fri Nov 12 2021 - 09:20:20 CST)
    - Re:Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 è¾›å¿—å®� (Fri Nov 12 2021 - 10:15:57 CST)
    - Re: Re:Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238 Kushal Raj Roy (Fri Nov 12 2021 - 11:13:21 CST)
Water molecules "flying away" in Gaussian calculation of "water int" step in FFTK Alexandre Suman de AraÃºjo (Wed Nov 10 2021 - 15:02:08 CST)
Fujitsu A64FX CPU processor-suitable NAMD Nikhil Maroli (Wed Nov 10 2021 - 13:27:32 CST)
- Re: Fujitsu A64FX CPU processor-suitable NAMD Vermaas, Josh (Wed Nov 10 2021 - 14:01:19 CST)
Colvar Flat-bottom potential "distanceXY" ROPÃ“N-PALACIOS G. (Wed Nov 10 2021 - 12:59:45 CST)
Protein simulations: why does the structure change so much? Francesco Coppola (Wed Nov 10 2021 - 10:25:47 CST)
SMD for predetermined Umbrella sampling Windows HANNAH MARIE BURTON (Mon Nov 08 2021 - 22:17:55 CST)
Why simulation running on linux is damn slow?? Amir Zeb (Mon Nov 08 2021 - 19:31:12 CST)
- Re: Why simulation running on linux is damn slow?? Vermaas, Josh (Mon Nov 08 2021 - 19:57:14 CST)
  - Re: Why simulation running on linux is damn slow?? Vermaas, Josh (Tue Nov 09 2021 - 10:58:01 CST)
- Re: Why simulation running on linux is damn slow?? Natalia Ostrowska (Wed Nov 10 2021 - 09:02:01 CST)
Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies JÃ©rÃ´me HÃ©nin (Fri Nov 05 2021 - 11:12:18 CDT)
- Re: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies yjcoshc (Fri Nov 05 2021 - 11:53:09 CDT)
  - Re: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies JÃ©rÃ´me HÃ©nin (Fri Nov 05 2021 - 12:10:35 CDT)
    - Re: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies JÃ©rÃ´me HÃ©nin (Fri Nov 05 2021 - 12:13:48 CDT)
    - Re: Bug advisory and workaround: alchemical FEP with IDWS can give wrong comparison energies yjcoshc (Fri Nov 05 2021 - 16:20:59 CDT)
REST2 soluteScalingFactor fluctuating between runs Ethan Croitoru (Tue Nov 02 2021 - 17:21:17 CDT)
Error Tolerance David Tang (Mon Nov 01 2021 - 16:33:01 CDT)
- Re: Error Tolerance Vermaas, Josh (Mon Nov 01 2021 - 18:11:26 CDT)
CONVERT PSF to TOP grimaces ROPÃ“N-PALACIOS G. (Sun Oct 31 2021 - 14:10:14 CDT)
- Re: CONVERT PSF to TOP grimaces Vermaas, Josh (Sun Oct 31 2021 - 15:02:48 CDT)
  - Re: CONVERT PSF to TOP grimaces Vermaas, Josh (Sun Oct 31 2021 - 15:53:27 CDT)
unable to run NAMD+ORCA on more than 1 cpu jing liang (Sat Oct 30 2021 - 13:09:24 CDT)
Trouble in fep.tcl file for FEP run in NAMD SYEDA SABIHA SULTANA LUBNA . (Sat Oct 30 2021 - 02:02:39 CDT)
- Re: Trouble in fep.tcl file for FEP run in NAMD JÃ©rÃ´me HÃ©nin (Tue Nov 02 2021 - 06:33:41 CDT)
Rattle algorithm failure while restarting metadynamics simulation Monika Kumari (Fri Oct 29 2021 - 09:40:13 CDT)
- Re: Rattle algorithm failure while restarting metadynamics simulation Giacomo Fiorin (Fri Oct 29 2021 - 10:01:01 CDT)
  - Re: Rattle algorithm failure while restarting metadynamics simulation Monika Kumari (Fri Oct 29 2021 - 23:43:56 CDT)
RMSD and RMSF of ligand Only Mi Yang (Thu Oct 28 2021 - 04:48:37 CDT)
- Re: RMSD and RMSF of ligand Only Natalia Ostrowska (Thu Oct 28 2021 - 06:33:24 CDT)
  - Re: RMSD and RMSF of ligand Only Natalia Ostrowska (Thu Oct 28 2021 - 06:42:29 CDT)
    - Re: RMSD and RMSF of ligand Only Mi Yang (Thu Oct 28 2021 - 08:35:40 CDT)
Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Oct 27 2021 - 14:43:12 CDT)
- Re: Error: keyword "abf" found without configuration Michael Robinson (Wed Oct 27 2021 - 19:27:57 CDT)
  - Re: Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Nov 10 2021 - 10:39:56 CST)
Script for contact Vs Freq Mi Yang (Thu Oct 21 2021 - 12:41:06 CDT)
Re: vmd-l: Fwd: Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Thu Oct 21 2021 - 04:15:56 CDT)
- Re: vmd-l: Fwd: Fwd: impropers for protonated 1-methyladenosine Francesco Pietra (Thu Oct 21 2021 - 07:56:06 CDT)
NAMD3 information ROPÃ“N-PALACIOS G. (Mon Oct 18 2021 - 17:14:47 CDT)
- Re: NAMD3 information Vermaas, Josh (Mon Oct 18 2021 - 19:08:49 CDT)
Addendum Francesco Pietra (Mon Oct 18 2021 - 15:03:31 CDT)
Ewald for charged systems Dongyue Liang (Mon Oct 18 2021 - 12:55:27 CDT)
impropers for protonated 1-methyladenosine Francesco Pietra (Mon Oct 18 2021 - 02:38:14 CDT)
- Re: impropers for protonated 1-methyladenosine Josh Vermaas (Mon Oct 18 2021 - 15:23:30 CDT)
  - Re: impropers for protonated 1-methyladenosine Francesco Pietra (Tue Oct 19 2021 - 02:32:21 CDT)
Namd3 error message Maria Kontoyianni (Fri Oct 15 2021 - 12:12:36 CDT)
Re: MD run terminated with singnal 11 Alessandro Ruda (Fri Oct 15 2021 - 07:04:30 CDT)
- Re: Re: MD run terminated with singnal 11 Josh Vermaas (Fri Oct 15 2021 - 08:30:05 CDT)
  - Re: Re: MD run terminated with singnal 11 Alessandro Ruda (Fri Oct 15 2021 - 08:56:04 CDT)
    - Re: Re: MD run terminated with singnal 11 Alessandro Ruda (Tue Oct 19 2021 - 11:32:23 CDT)
    - Re: Re: MD run terminated with singnal 11 Jeff Comer (Tue Oct 19 2021 - 19:32:22 CDT)
Job stopped without any error message (probably a load balancing issue?) Haohao Fu (Fri Oct 15 2021 - 00:14:33 CDT)
- Re: Job stopped without any error message (probably a load balancing issue?) Natalia Ostrowska (Fri Oct 15 2021 - 01:35:40 CDT)
  - Re: Job stopped without any error message (probably a load balancing issue?) Haohao Fu (Fri Oct 15 2021 - 03:10:38 CDT)
    - Re: Job stopped without any error message (probably a load balancing issue?) Natalia Ostrowska (Fri Oct 15 2021 - 04:18:40 CDT)
[containerising NAMD with Singularity] Maxim Abalenkov (Wed Oct 13 2021 - 04:28:36 CDT)
- Re: [containerising NAMD with Singularity] Giacomo Fiorin (Wed Oct 13 2021 - 08:25:58 CDT)
- Re: [containerising NAMD with Singularity] Josh Vermaas (Wed Oct 13 2021 - 08:57:23 CDT)
MMPBSA standard deviation Nancy Singh (Mon Oct 11 2021 - 06:53:26 CDT)
Query about post-process of DCD PREMANANDA BASAK (Thu Oct 07 2021 - 07:10:34 CDT)
- Re: Query about post-process of DCD Diship Srivastava (Thu Oct 07 2021 - 08:07:53 CDT)
NAMD Cuda on more than one node Alexei Rossokhin (Wed Oct 06 2021 - 02:24:16 CDT)
QM/MM biding free energy Mi Yang (Sun Oct 03 2021 - 09:58:44 CDT)
how can email dcd files Asmi Mahmood (Sat Oct 02 2021 - 06:02:11 CDT)
- Re: how can email dcd files Hemanth Haridas (Sat Oct 02 2021 - 06:13:20 CDT)
- Re: how can email dcd files Ashkan Shekaari (Sat Oct 02 2021 - 06:51:01 CDT)
Salt bridge selection Vidhya Sankar (Fri Oct 01 2021 - 21:25:01 CDT)
Re: Simulation Box Size & Simulation speed Fateme Ghadirian (Thu Sep 30 2021 - 16:40:12 CDT)
Simulation Box Size & Simulation speed Fateme Ghadirian (Thu Sep 30 2021 - 11:15:00 CDT)
ERROR: Atoms moving too fast; simulation has become unstable. Hasith Sathsindu (Wed Sep 29 2021 - 13:23:57 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:36:27 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:40:38 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:50:34 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:53:15 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable. Ashkan Shekaari (Wed Sep 29 2021 - 15:54:14 CDT)
QM/MM live solvent selection - segmentation fault (with ORCA) Oleksii Zdorevskyi (Tue Sep 28 2021 - 10:39:18 CDT)
- Re: QM/MM live solvent selection - segmentation fault (with ORCA) Oleksii Zdorevskyi (Tue Sep 28 2021 - 14:11:06 CDT)
Replica run of Constant pH MD Diship Srivastava (Tue Sep 28 2021 - 09:58:32 CDT)
- Re: Replica run of Constant pH MD Brian Radak (Tue Sep 28 2021 - 20:12:06 CDT)
about compilation Vidhya Sankar (Tue Sep 28 2021 - 02:16:04 CDT)
- Re: about compilation Giacomo Fiorin (Tue Sep 28 2021 - 08:05:14 CDT)
SMD in lipid Ishaan Roy (Fri Sep 24 2021 - 12:01:20 CDT)
- Re: SMD in lipid Ashkan Shekaari (Fri Sep 24 2021 - 15:53:23 CDT)
Metadynamics Farag Mosa (Thu Sep 23 2021 - 14:21:37 CDT)
Switching from GPU to CPU: failing with too many CPUs? Smith, Harper E. (Thu Sep 23 2021 - 10:41:47 CDT)
performance scaling of CUDA accelerated NAMD over multiple nodes Vlad Cojocaru (Fri Sep 17 2021 - 05:11:56 CDT)
- Re: performance scaling of CUDA accelerated NAMD over multiple nodes Vermaas, Josh (Fri Sep 17 2021 - 07:31:45 CDT)
  - Re: performance scaling of CUDA accelerated NAMD over multiple nodes Vlad Cojocaru (Fri Sep 17 2021 - 08:05:40 CDT)
vdW for atom NRN1 Francesco Pietra (Tue Sep 14 2021 - 08:28:38 CDT)
- Fwd: vdW for atom NRN1 Francesco Pietra (Tue Sep 14 2021 - 08:46:04 CDT)
  - Re: Fwd: vdW for atom NRN1 Mohammad Mehdi Pirnia (Tue Sep 14 2021 - 09:25:54 CDT)
- Re: vdW for atom NRN1 Ashkan Shekaari (Tue Sep 14 2021 - 08:53:17 CDT)
  - Re: vdW for atom NRN1 Francesco Pietra (Tue Sep 14 2021 - 09:26:02 CDT)
MMPBSA calculation using CAFE plugin vmd Nancy Singh (Tue Sep 14 2021 - 06:27:32 CDT)
- Re: MMPBSA calculation using CAFE plugin vmd Pratik Narain Srivastava (Tue Sep 14 2021 - 07:03:41 CDT)
Problem with speed of QMMM (namd2-ORCA) Herald Delis (Thu Sep 09 2021 - 05:51:14 CDT)
- Re: Problem with speed of QMMM (namd2-ORCA) Marcelo C. R. Melo (Thu Sep 09 2021 - 12:09:00 CDT)
  - Re: Problem with speed of QMMM (namd2-ORCA) Herald Delis (Thu Sep 09 2021 - 19:59:56 CDT)
    - Re: Problem with speed of QMMM (namd2-ORCA) Marcelo C. R. Melo (Sat Sep 11 2021 - 00:27:46 CDT)
    - Re: Problem with speed of QMMM (namd2-ORCA) Herald Delis (Sun Sep 12 2021 - 00:22:07 CDT)
Patch for non protonated lysine Francesco Pietra (Wed Sep 08 2021 - 04:19:49 CDT)
- Re: Patch for non protonated lysine Jeff Comer (Wed Sep 08 2021 - 11:28:38 CDT)
  - Re: Patch for non protonated lysine Francesco Pietra (Wed Sep 08 2021 - 12:01:17 CDT)
Re: namd-l digest V1 #3135 Venkatareddy Dadireddy (Wed Sep 08 2021 - 02:48:33 CDT)
Merge ABF windows SÃ©bastien Hoyas (Wed Sep 08 2021 - 01:53:43 CDT)
- Re: Merge ABF windows JÃ©rÃ´me HÃ©nin (Tue Sep 21 2021 - 07:55:34 CDT)
  - Re: Merge ABF windows JÃ©rÃ´me HÃ©nin (Tue Sep 21 2021 - 09:18:36 CDT)
    - Re: Merge ABF windows RenÃ© Hafner TUK (Thu Sep 23 2021 - 11:15:08 CDT)
GaMD is slower on GPU compared to cMD Venkatareddy Dadireddy (Mon Sep 06 2021 - 11:15:00 CDT)
- Re: GaMD is slower on GPU compared to cMD Josh Vermaas (Tue Sep 07 2021 - 09:08:00 CDT)
Re: Assunto: Re: Binary coordinates NAMD 2.14 Vermaas, Josh (Fri Sep 03 2021 - 19:05:43 CDT)
Binary coordinates NAMD 2.14 oivalf_nix_at_yahoo.com (Fri Sep 03 2021 - 14:05:39 CDT)
- Re: Binary coordinates NAMD 2.14 Giacomo Fiorin (Fri Sep 03 2021 - 14:20:57 CDT)
  - Re: Binary coordinates NAMD 2.14 oivalf_nix_at_yahoo.com (Fri Sep 03 2021 - 14:58:55 CDT)
    - Re: Binary coordinates NAMD 2.14 Josh Vermaas (Fri Sep 03 2021 - 15:42:44 CDT)
(no subject) Krithika Unmesh (Thu Sep 02 2021 - 09:40:41 CDT)
- Re: ROPÃ“N-PALACIOS G. (Thu Sep 02 2021 - 09:48:15 CDT)
Re: Problem with running replica-exchange umbrella sampling of polarizable system zeynab hosseini (Thu Sep 02 2021 - 02:12:43 CDT)
- Re: Problem with running replica-exchange umbrella sampling of polarizable system Hemanth Haridas (Thu Sep 02 2021 - 04:36:46 CDT)
  - Re: Problem with running replica-exchange umbrella sampling of polarizable system zeynab hosseini (Thu Sep 02 2021 - 04:40:05 CDT)
- Re: Problem with running replica-exchange umbrella sampling of polarizable system zeynab hosseini (Thu Sep 02 2021 - 04:38:30 CDT)
Modifying a DRUDE pdb file and producing a new psf file HANNAH MARIE BURTON (Wed Sep 01 2021 - 11:25:17 CDT)
Problem with running replica-exchange umbrella sampling of polarizable system zeynab hosseini (Wed Sep 01 2021 - 05:20:30 CDT)
Free energy calculations Nancy Singh (Mon Aug 30 2021 - 08:59:47 CDT)
- Re: Free energy calculations Pratik Narain Srivastava (Mon Aug 30 2021 - 09:08:56 CDT)
Unrealistically High Keq in eABF Seperation Ishaan Roy (Tue Aug 24 2021 - 17:23:39 CDT)
- Re: Unrealistically High Keq in eABF Seperation Peter Freddolino (Wed Aug 25 2021 - 22:27:46 CDT)
  - RE: Unrealistically High Keq in eABF Seperation Ishaan Roy (Thu Aug 26 2021 - 02:28:47 CDT)
    - Re: Unrealistically High Keq in eABF Seperation Chris Chipot (Thu Aug 26 2021 - 02:41:52 CDT)
    - RE: Unrealistically High Keq in eABF Seperation Ishaan Roy (Wed Sep 08 2021 - 13:46:47 CDT)
Asymmetric concentration gradient Ropon-Palacios G. (Mon Aug 23 2021 - 21:08:16 CDT)
- Re: Asymmetric concentration gradient Gumbart, JC (Mon Aug 23 2021 - 23:05:19 CDT)
  - Re: Asymmetric concentration gradient Ropon-Palacios G. (Mon Aug 23 2021 - 23:10:52 CDT)
sphingosine topology and parameter files Capponi, Sara (Mon Aug 23 2021 - 12:22:20 CDT)
psfgen problem for membrane, LPSA and bacterial lipids Mohammad Mehdi Pirnia (Sat Aug 21 2021 - 19:43:21 CDT)
- Error: psfgen) unknown atom type H Mohammad Mehdi Pirnia (Thu Aug 26 2021 - 20:14:02 CDT)
  - Re: Error: psfgen) unknown atom type H Gumbart, JC (Fri Aug 27 2021 - 10:27:52 CDT)
eABF Improper Protein Seperation Ishaan Roy (Tue Aug 17 2021 - 15:40:56 CDT)
- Re: eABF Improper Protein Seperation Jeff Comer (Wed Aug 18 2021 - 16:24:05 CDT)
eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling RenÃ© Hafner TUK (Sat Aug 14 2021 - 10:22:37 CDT)
- Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling Giacomo Fiorin (Sat Aug 14 2021 - 12:17:53 CDT)
  - Re: eABF 3D sampling using distance Colvars + X and Y: averaged PMF difference to 1D sampling RenÃ© Hafner TUK (Sat Aug 14 2021 - 12:28:46 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CD2R6A LPA1 zeynab hosseini (Fri Aug 13 2021 - 03:26:03 CDT)
Problem in running constant pH NAMD job Diship Srivastava (Wed Aug 11 2021 - 11:02:32 CDT)
- Re: Problem in running constant pH NAMD job Brian Radak (Thu Aug 12 2021 - 12:29:25 CDT)
  - Re: Problem in running constant pH NAMD job Diship Srivastava (Sat Aug 14 2021 - 09:24:49 CDT)
    - Re: Problem in running constant pH NAMD job Brian Radak (Sat Aug 14 2021 - 10:22:16 CDT)
MD simulation Ruturaj warake (Sun Aug 08 2021 - 02:12:11 CDT)
- Re: MD simulation Pratik Narain Srivastava (Sun Aug 08 2021 - 02:15:35 CDT)
  - Re: MD simulation Ruturaj warake (Sun Aug 08 2021 - 09:44:27 CDT)
    - Re: MD simulation ROPÃ“N-PALACIOS G. (Tue Aug 10 2021 - 23:33:54 CDT)
Compiling issue: selfcompiled NAMD2.14 multicore version factor ~2x slower RenÃ© Hafner TUK (Sat Aug 07 2021 - 14:16:44 CDT)
- Re: Compiling issue: selfcompiled NAMD2.14 multicore version factor ~2x slower Giacomo Fiorin (Sat Aug 07 2021 - 15:40:42 CDT)
  - Re: Compiling issue: selfcompiled NAMD2.14 multicore version factor ~2x slower - SOLVED RenÃ© Hafner TUK (Sat Aug 07 2021 - 17:44:01 CDT)
Numsteps or Runs? Ruturaj warake (Wed Aug 04 2021 - 10:51:48 CDT)
- Re: Numsteps or Runs? Ashkan Shekaari (Wed Aug 04 2021 - 13:00:44 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS samaneh ghanbari (Tue Aug 03 2021 - 09:05:36 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS ROPÃ“N-PALACIOS G. (Tue Aug 03 2021 - 09:15:53 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Josh Vermaas (Tue Aug 03 2021 - 09:16:45 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Abhishek TYAGI (Wed Aug 04 2021 - 22:32:11 CDT)
Running NAMD 3.0 Ruturaj warake (Tue Aug 03 2021 - 04:46:14 CDT)
- Re: Running NAMD 3.0 Oscar Bastidas (Tue Aug 03 2021 - 04:57:01 CDT)
constant pH with NAMD3 Jeff Comer (Mon Aug 02 2021 - 22:36:19 CDT)
- Re: constant pH with NAMD3 Jeff Comer (Mon Aug 02 2021 - 22:47:53 CDT)
  - Re: constant pH with NAMD3 Brian Radak (Tue Aug 03 2021 - 07:25:07 CDT)
Reducing the system size Ruturaj warake (Mon Aug 02 2021 - 09:59:32 CDT)
- Re: Reducing the system size ashkan shekaari (Mon Aug 02 2021 - 16:15:42 CDT)
  - Re: Reducing the system size RenÃ© Hafner TUK (Mon Aug 02 2021 - 16:37:12 CDT)
Mail About error in CV Vidhya Sankar (Mon Aug 02 2021 - 03:31:16 CDT)
- Re: Mail About error in CV Giacomo Fiorin (Mon Aug 02 2021 - 09:51:37 CDT)
Problem with creating Drude-compatible .psf file for amino acid zeynab hosseini (Fri Jul 30 2021 - 07:05:13 CDT)
Fatal Error: Error in the configuration file Amir Zeb (Fri Jul 30 2021 - 01:06:18 CDT)
- Re: Fatal Error: Error in the configuration file RenÃ© Hafner TUK (Fri Jul 30 2021 - 01:18:07 CDT)
  - Re: Fatal Error: Error in the configuration file ashkan shekaari (Fri Jul 30 2021 - 04:43:18 CDT)
    - Re: Fatal Error: Error in the configuration file ashkan shekaari (Fri Jul 30 2021 - 04:44:42 CDT)
    - Re: Fatal Error: Error in the configuration file ashkan shekaari (Fri Jul 30 2021 - 04:49:02 CDT)
mail about error in namd configuration file Vidhya Sankar (Thu Jul 29 2021 - 07:50:15 CDT)
- Re: mail about error in namd configuration file Giacomo Fiorin (Thu Jul 29 2021 - 08:31:43 CDT)
about usage of eABF method Vidhya Sankar (Thu Jul 29 2021 - 04:10:52 CDT)
- Re: about usage of eABF method Giacomo Fiorin (Thu Jul 29 2021 - 08:10:47 CDT)
NUMA Node and CUDA GPU Acceleration Gawtak Kim (Thu Jul 29 2021 - 02:23:09 CDT)
Mail about path CV Vidhya Sankar (Wed Jul 28 2021 - 05:09:19 CDT)
- Re: Mail about path CV Giacomo Fiorin (Wed Jul 28 2021 - 08:22:44 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER samaneh ghanbari (Tue Jul 27 2021 - 23:03:37 CDT)
- Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER Ashkan Shekaari (Wed Jul 28 2021 - 04:34:30 CDT)
MMGBSA binding free energy by MolAICal and NAMD molaical (Tue Jul 27 2021 - 12:20:38 CDT)
Query in running NAMD Ruturaj warake (Mon Jul 26 2021 - 11:27:59 CDT)
Error in running simulation Ruturaj warake (Mon Jul 26 2021 - 08:29:30 CDT)
- Re: Error in running simulation Diship Srivastava (Mon Jul 26 2021 - 08:33:36 CDT)
- Re: Error in running simulation RenÃ© Hafner TUK (Mon Jul 26 2021 - 08:34:43 CDT)
- Re: Error in running simulation Ruturaj warake (Mon Jul 26 2021 - 10:10:59 CDT)
  - Re: Error in running simulation RenÃ© Hafner TUK (Mon Jul 26 2021 - 10:31:31 CDT)
    - Re: Error in running simulation Ruturaj warake (Mon Jul 26 2021 - 11:02:41 CDT)
Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? zeynab hosseini (Sun Jul 25 2021 - 14:07:42 CDT)
- Re: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? Victor Kwan (Mon Jul 26 2021 - 18:31:00 CDT)
  - Re: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? zeynab hosseini (Tue Jul 27 2021 - 11:27:59 CDT)
    - Re: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? Michael Robinson (Wed Jul 28 2021 - 20:57:29 CDT)
    - Re: Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes? zeynab hosseini (Thu Jul 29 2021 - 10:36:23 CDT)
namd-I: Request for help in error fixing Dr. Anupama Tiwari (Sun Jul 25 2021 - 09:07:10 CDT)
- Re: namd-I: Request for help in error fixing Ashkan Shekaari (Sun Jul 25 2021 - 10:06:27 CDT)
  - Re: namd-I: Request for help in error fixing Dr. Anupama Tiwari (Mon Jul 26 2021 - 08:07:10 CDT)
About Meta dynamics Vidhya Sankar (Thu Jul 22 2021 - 08:18:34 CDT)
- Re: About Meta dynamics Giacomo Fiorin (Thu Jul 22 2021 - 08:29:28 CDT)
Request for help on error fixing Amir Zeb (Thu Jul 22 2021 - 01:10:49 CDT)
- Re: Request for help on error fixing Ashkan Shekaari (Thu Jul 22 2021 - 04:34:19 CDT)
NAMD download form unavailable? Renfro, Michael (Wed Jul 21 2021 - 15:18:31 CDT)
- Re: NAMD download form unavailable? Renfro, Michael (Thu Jul 22 2021 - 08:29:30 CDT)
Please ignore previous poor formatted: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. Ryan Woltz (Tue Jul 20 2021 - 18:14:31 CDT)
- Re: Please ignore previous poor formatted: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. Vermaas, Josh (Wed Jul 21 2021 - 09:56:47 CDT)
  - Re: Please ignore previous poor formatted: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. Ryan Woltz (Fri Jul 30 2021 - 16:57:27 CDT)
difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. Ryan Woltz (Tue Jul 20 2021 - 18:06:14 CDT)
- Re: difficulty converting namd2 channel system to namd3 Atom velocity too fast, box too small errors. Gumbart, JC (Tue Jul 27 2021 - 10:52:32 CDT)
Constraints required for alpha helix secondary structure Diship Srivastava (Fri Jul 16 2021 - 05:51:56 CDT)
- Re: Constraints required for alpha helix secondary structure Ashkan Shekaari (Fri Jul 16 2021 - 11:08:33 CDT)
  - Re: Constraints required for alpha helix secondary structure Diship Srivastava (Fri Jul 16 2021 - 11:21:42 CDT)
- Re: [External Email] Constraints required for alpha helix secondary structure Sandeep Dash (Fri Jul 16 2021 - 14:38:52 CDT)
wrap is On to Diffusion phenomena ? Ropon-Palacios G. (Thu Jul 15 2021 - 17:45:26 CDT)
- Re: wrap is On to Diffusion phenomena ? JÃ©rÃ´me HÃ©nin (Tue Jul 27 2021 - 07:13:34 CDT)
MMGBSA binding free energy by MolAICal and NAMD Mi Yang (Wed Jul 14 2021 - 13:42:09 CDT)
- Re: MMGBSA binding free energy by MolAICal and NAMD molaical (Tue Jul 27 2021 - 12:36:12 CDT)
- Re: MMGBSA binding free energy by MolAICal and NAMD molaical (Tue Jul 27 2021 - 12:38:14 CDT)
simulations space partitioning parameters Nancy Singh (Wed Jul 14 2021 - 06:45:55 CDT)
- Re: simulations space partitioning parameters Josh Vermaas (Wed Jul 14 2021 - 08:52:17 CDT)
Protein-ligand complex is coming out of the water box Nancy Singh (Wed Jul 14 2021 - 06:16:58 CDT)
- Re: Protein-ligand complex is coming out of the water box RenÃ© Hafner TUK (Wed Jul 14 2021 - 06:27:23 CDT)
- Re: Protein-ligand complex is coming out of the water box Ashkan Shekaari (Wed Jul 14 2021 - 06:30:22 CDT)
question about free energy calculation through FEP method in NAMD M. A (Wed Jul 14 2021 - 01:35:05 CDT)
- Re: question about free energy calculation through FEP method in NAMD JÃ©rÃ´me HÃ©nin (Wed Jul 14 2021 - 05:31:05 CDT)
- Re: question about free energy calculation through FEP method in NAMD Ashkan Shekaari (Wed Jul 14 2021 - 05:42:02 CDT)
  - Re: question about free energy calculation through FEP method in NAMD Ashkan Shekaari (Wed Jul 14 2021 - 05:50:01 CDT)
  - Re: question about free energy calculation through FEP method in NAMD M. A (Wed Jul 14 2021 - 14:40:56 CDT)
question about free energy calculation through FEP method in NAMD M. A (Tue Jul 13 2021 - 08:41:10 CDT)
Temperature accelerated MD with Colvar or TclForces Ropon-Palacios G. (Fri Jul 09 2021 - 18:49:40 CDT)
Binding free energy analysis at specific time interval during MD trajectory Mi Yang (Thu Jul 08 2021 - 13:48:20 CDT)
- Re: Binding free energy analysis at specific time interval during MD trajectory Pratik Narain Srivastava (Thu Jul 08 2021 - 14:56:13 CDT)
Simulation of protein-lipid complex by NAMD with OPLS3e ff? Amir Zeb (Tue Jul 06 2021 - 22:04:42 CDT)
Membrane Protein Flipping in ABF Ishaan Roy (Wed Jun 30 2021 - 20:44:23 CDT)
- Re: Membrane Protein Flipping in ABF Giacomo Fiorin (Wed Jun 30 2021 - 20:52:49 CDT)
  - Re: Membrane Protein Flipping in ABF Giacomo Fiorin (Wed Jul 07 2021 - 09:31:19 CDT)
Inquiry about NAMD beta Sandeep Dash (Wed Jun 30 2021 - 10:48:36 CDT)
Constant ph md Diship Srivastava (Mon Jun 28 2021 - 08:02:29 CDT)
- Re: Constant ph md Brian Radak (Mon Jun 28 2021 - 15:07:39 CDT)
NAMD jobs in SLURM environment, not entering queueing system Prathit Chatterjee (Mon Jun 28 2021 - 03:54:22 CDT)
- Re: NAMD jobs in SLURM environment, not entering queueing system RenÃ© Hafner TUK (Mon Jun 28 2021 - 04:03:46 CDT)
  - Re: NAMD jobs in SLURM environment, not entering queueing system RenÃ© Hafner TUK (Mon Jun 28 2021 - 04:27:06 CDT)
  - Re: NAMD jobs in SLURM environment, not entering queueing system Prathit Chatterjee (Thu Jul 01 2021 - 10:41:31 CDT)
Potential NAMD Update Bug Shiv Seshan (Fri Jun 25 2021 - 15:17:43 CDT)
- Re: Potential NAMD Update Bug yjcoshc (Fri Jun 25 2021 - 21:48:14 CDT)
NAMD on AMD GPU jing liang (Wed Jun 23 2021 - 05:06:12 CDT)
- Re: NAMD on AMD GPU jing liang (Thu Jun 24 2021 - 14:58:57 CDT)
  - Re: NAMD on AMD GPU Josh Vermaas (Thu Jun 24 2021 - 15:21:01 CDT)
    - Re: NAMD on AMD GPU jing liang (Thu Jun 24 2021 - 23:27:11 CDT)
    - Re: NAMD on AMD GPU Josh Vermaas (Fri Jun 25 2021 - 08:18:02 CDT)
Visualizing REST2 Simulation Ethan Croitoru (Mon Jun 21 2021 - 19:42:43 CDT)
Re: Jarzynski calculate ROPÃ“N-PALACIOS G. (Fri Jun 18 2021 - 14:20:07 CDT)
Jarzynski calculate Ropon-Palacios G. (Fri Jun 18 2021 - 00:29:42 CDT)
libcufft_static.a error Frank Duan (Wed Jun 16 2021 - 09:06:18 CDT)
Dual topology FEP Ropon-Palacios G. (Tue Jun 15 2021 - 19:24:46 CDT)
Hydrogen Mass Repartitioning -> NVE energy loss due to rigidBonds Maximilian Ebert (Mon Jun 14 2021 - 17:00:40 CDT)
Protein equilibration Nadira Khatoon (Mon Jun 07 2021 - 09:56:58 CDT)
Problem of calculating PMF changed by tilt angle using extended ABF Namho Kim (Sun Jun 06 2021 - 21:18:44 CDT)
- Re: Problem of calculating PMF changed by tilt angle using extended ABF JÃ©rÃ´me HÃ©nin (Mon Jun 07 2021 - 05:30:26 CDT)
PSF file format Maximilian Ebert (Fri Jun 04 2021 - 12:10:00 CDT)
- Re: PSF file format Josh Vermaas (Fri Jun 04 2021 - 12:48:41 CDT)
  - Re: PSF file format Axel Kohlmeyer (Fri Jun 04 2021 - 12:59:48 CDT)
Glycoprotein-flavonoid complex oivalf_nix_at_yahoo.com (Wed Jun 02 2021 - 07:44:06 CDT)
How to deal with trajectories from RAMD in NAMD? ÍõÒÁÇï (Thu May 27 2021 - 20:54:58 CDT)
A position of a computational chemist is open in Cambridge, MA Alexander Balaeff (Thu May 27 2021 - 13:11:55 CDT)
question about In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD M. A (Thu May 27 2021 - 02:30:54 CDT)
- Re: question about In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD JÃ©rÃ´me HÃ©nin (Thu May 27 2021 - 04:28:37 CDT)
  - Re: question about In silico alchemy: tutorial for alchemical free-energy perturbation calculations with NAMD M. A (Fri May 28 2021 - 09:44:14 CDT)
FATAL ERROR: Error in the collective variables module è¾›å¿—å®� (Wed May 26 2021 - 05:19:28 CDT)
- Re: FATAL ERROR: Error in the collective variables module yjcoshc (Wed May 26 2021 - 05:43:20 CDT)
FEP with cudaSOAIntegrate in NAMD 3.0alph9 Kevin Chan (Tue May 25 2021 - 08:39:57 CDT)
- Re: FEP with cudaSOAIntegrate in NAMD 3.0alph9 yjcoshc (Wed May 26 2021 - 06:43:16 CDT)
  - Re: FEP with cudaSOAIntegrate in NAMD 3.0alph9 Kevin Chan (Sat Jun 12 2021 - 08:32:06 CDT)
Regarding Parameter file Nadira Khatoon (Sun May 23 2021 - 12:14:39 CDT)
- Re: Regarding Parameter file RenÃ© Hafner TUK (Mon May 24 2021 - 03:51:05 CDT)
  - Re: Regarding Parameter file Nadira Khatoon (Mon May 24 2021 - 09:26:49 CDT)
    - Re: Regarding Parameter file RenÃ© Hafner TUK (Mon May 24 2021 - 09:51:14 CDT)
Tclforces Ropon-Palacios G. (Fri May 21 2021 - 20:25:10 CDT)
Cannot run OPC solvated system on NAMD3 Sara Omar (Wed May 19 2021 - 23:24:59 CDT)
- Re: Cannot run OPC solvated system on NAMD3 David Hardy (Fri May 21 2021 - 00:43:32 CDT)
Membrane protein SHEYLA ESTHER CARMEN SIFUENTES (Tue May 18 2021 - 22:48:47 CDT)
VMD and NAMD surveys will be coming soon David Hardy (Tue May 18 2021 - 14:26:59 CDT)
Getting the z coordinate Isaac Asare Kwaku (Mon May 17 2021 - 10:59:22 CDT)
- Re: Getting the z coordinate Diship Srivastava (Mon May 17 2021 - 12:10:56 CDT)
- Re: Getting the z coordinate Pawel Kedzierski (Mon May 17 2021 - 12:17:31 CDT)
  - Re: Getting the z coordinate Isaac Asare Kwaku (Mon May 17 2021 - 12:21:14 CDT)
Re: Re: Re-center membrane protein Ropon-Palacios G. (Fri May 14 2021 - 12:21:20 CDT)
- Re: Re: Re-center membrane protein Ramon Mendoza Uriarte (Fri May 14 2021 - 12:51:41 CDT)
Re-center membrane protein Ropon-Palacios G. (Fri May 14 2021 - 12:02:34 CDT)
- Re: Re-center membrane protein Ramon Mendoza Uriarte (Fri May 14 2021 - 12:18:13 CDT)
newby in NAMD joseph pareti (Fri May 14 2021 - 11:12:45 CDT)
- Re: newby in NAMD Vermaas, Josh (Fri May 14 2021 - 12:05:20 CDT)
- Re: newby in NAMD Peter Freddolino (Fri May 14 2021 - 13:42:43 CDT)
Metadynamics problems Alessandro Ruda (Fri May 14 2021 - 04:48:18 CDT)
- Re: Metadynamics problems Giacomo Fiorin (Fri May 14 2021 - 10:43:08 CDT)
  - Re: Metadynamics problems Alessandro Ruda (Mon May 17 2021 - 11:51:10 CDT)
    - Re: Metadynamics problems Giacomo Fiorin (Tue May 25 2021 - 09:29:12 CDT)
Quantifying Error for Free Energy Calculations Ethan Croitoru (Wed May 05 2021 - 12:57:20 CDT)
- Re: Quantifying Error for Free Energy Calculations Chris Chipot (Thu May 06 2021 - 08:18:32 CDT)
Mail about Alchemify error Vidhya Sankar (Wed May 05 2021 - 08:36:17 CDT)
Mail about error in Alchemify programme in namd Vidhya Sankar (Tue May 04 2021 - 07:30:53 CDT)
- Re: Mail about error in Alchemify programme in namd JÃ©rÃ´me HÃ©nin (Tue May 04 2021 - 16:07:50 CDT)
System with two membranes JosÃ© VillalaÃn (Fri Apr 30 2021 - 03:54:08 CDT)
- Re: System with two membranes Vermaas, Josh (Fri Apr 30 2021 - 08:59:01 CDT)
  - Re: System with two membranes Giacomo Fiorin (Fri Apr 30 2021 - 10:03:41 CDT)
Truncated solvate plugin Ropon-Palacios G. (Thu Apr 22 2021 - 22:17:15 CDT)
A postdoctoral position in Atlanta, GA, USA Ivaylo Nikolaev Ivanov (Wed Apr 28 2021 - 20:40:56 CDT)
- Re: A postdoctoral position in Atlanta, GA, USA Kushal Raj Roy (Tue May 18 2021 - 08:42:13 CDT)
Efficiency of constant-pH simulations? Smith, Harper E. (Wed Apr 28 2021 - 18:52:30 CDT)
- Re: Efficiency of constant-pH simulations? Brian Radak (Thu Apr 29 2021 - 07:17:24 CDT)
graphene sheet as a rigid piston SHIVAM TIWARI (Wed Apr 28 2021 - 12:38:22 CDT)
- Re: graphene sheet as a rigid piston Hemanth Haridas (Fri Apr 30 2021 - 05:28:47 CDT)
  - Re: graphene sheet as a rigid piston Dalhaimer, Paul Matthew (Fri Apr 30 2021 - 06:24:39 CDT)
Umbrella windows ROPÃ“N-PALACIOS G. (Sat Apr 24 2021 - 12:59:00 CDT)
Advice on hardware for NAMD Raman Preet Singh (Fri Apr 23 2021 - 04:09:25 CDT)
Meaning of the warning: Low global exclusion count! Pawel Kedzierski (Wed Apr 21 2021 - 06:01:05 CDT)
- Re: Meaning of the warning: Low global exclusion count! David Hardy (Wed Apr 21 2021 - 15:31:44 CDT)
  - Re: Meaning of the warning: Low global exclusion count! Pawel Kedzierski (Thu Apr 22 2021 - 08:21:08 CDT)
    - Re: Meaning of the warning: Low global exclusion count! David Hardy (Thu Apr 22 2021 - 14:15:40 CDT)
Error Analysis in Metadynamics Diship Srivastava (Tue Apr 20 2021 - 01:39:25 CDT)
- Re: Error Analysis in Metadynamics Miro Astore (Tue Apr 20 2021 - 02:35:11 CDT)
  - Re: Error Analysis in Metadynamics Giacomo Fiorin (Fri Apr 23 2021 - 10:57:34 CDT)
gpu performance Stefano Guglielmo (Mon Apr 19 2021 - 05:03:58 CDT)
- Re: gpu performance Vermaas, Josh (Mon Apr 19 2021 - 08:33:17 CDT)
Free Energy Calculations on Helical Dimer: Separation Run Snaps Back Ethan Croitoru (Sun Apr 18 2021 - 15:26:27 CDT)
- Re: Free Energy Calculations on Helical Dimer: Separation Run Snaps Back JÃ©rÃ´me HÃ©nin (Mon Apr 19 2021 - 11:04:49 CDT)
Using a graphene sheet as a rigid piston SHIVAM TIWARI (Sat Apr 17 2021 - 02:28:50 CDT)
Center trajectory with box dodecahedron Ropon-Palacios G. (Fri Apr 16 2021 - 13:52:11 CDT)
Installing NAMD in Ethernet (1Gbps) cluster Yasser Bruno Ruiz Blanco (Fri Apr 16 2021 - 04:15:08 CDT)
Empty PMF files after ABF simulation Shivansh Seth (Wed Apr 14 2021 - 23:01:16 CDT)
Re: Multi-node-gpu NAMD Vermaas, Josh (Wed Apr 14 2021 - 15:41:07 CDT)
Multi-node-gpu NAMD Ropon-Palacios G. (Wed Apr 14 2021 - 13:22:03 CDT)
- Re: Multi-node-gpu NAMD Axel Kohlmeyer (Wed Apr 14 2021 - 15:46:48 CDT)
QM/MM orbitals visualization jing liang (Tue Apr 13 2021 - 03:14:03 CDT)
A question about PME correction term in QM/MM Kendall Byler (Mon Apr 12 2021 - 10:58:19 CDT)
NAMD web/email outage today Tuesday 4/6 David Hardy (Tue Apr 06 2021 - 13:12:49 CDT)
Spherical restraints Almeida-Hernández, Yasser, Dr. (Tue Apr 06 2021 - 09:07:44 CDT)
- Re: Spherical restraints Giacomo Fiorin (Tue Apr 06 2021 - 10:06:58 CDT)
  - Re: Spherical restraints Almeida-Hernández, Yasser, Dr. (Tue Apr 06 2021 - 10:50:11 CDT)
    - Re: Spherical restraints Giacomo Fiorin (Tue Apr 06 2021 - 11:17:11 CDT)
  - Re: Spherical restraints Giacomo Fiorin (Tue Apr 06 2021 - 13:31:27 CDT)
Empty PMF files in ABF Shivansh Seth (Tue Apr 06 2021 - 07:19:04 CDT)
Ultra-violet environment simulation in NAMD Faisal, H M Nasrullah (Mon Apr 05 2021 - 10:55:08 CDT)
Picking a GPU for namd 3.0 Goedde, Chris (Thu Apr 01 2021 - 11:18:52 CDT)
- Re: Picking a GPU for namd 3.0 Vermaas, Josh (Thu Apr 01 2021 - 12:52:30 CDT)
comparing Classical and Accelerated MD results raghav singh (Tue Mar 30 2021 - 04:43:00 CDT)
potential bug while compiling the Windows version of NAMD Osvalds Verners (Thu Mar 25 2021 - 12:37:54 CDT)
- Re: potential bug while compiling the Windows version of NAMD David Hardy (Mon Mar 29 2021 - 18:37:07 CDT)
  - Re: potential bug while compiling the Windows version of NAMD Osvalds Verners (Mon Apr 05 2021 - 23:11:10 CDT)
    - Re: potential bug while compiling the Windows version of NAMD Osvalds Verners (Mon Apr 05 2021 - 23:18:16 CDT)
- Re: potential bug while compiling the Windows version of NAMD David Hardy (Wed Mar 31 2021 - 14:53:04 CDT)
(no subject) soumadwip ghosh (Thu Mar 25 2021 - 11:25:58 CDT)
Volumetric map simulations Carlo Guardiani (Thu Mar 25 2021 - 05:22:10 CDT)
- Re: Volumetric map simulations Vermaas, Josh (Thu Mar 25 2021 - 09:33:17 CDT)
  - Re: Volumetric map simulations Giacomo Fiorin (Thu Mar 25 2021 - 09:52:13 CDT)
how to properly end NAMD replica job on slurm batch system RenÃ© Hafner TUK (Wed Mar 24 2021 - 08:13:04 CDT)
- Re: how to properly end NAMD replica job on slurm batch system Vermaas, Josh (Wed Mar 24 2021 - 09:40:29 CDT)
  - Re: how to properly end NAMD replica job on slurm batch system RenÃ© Hafner TUK (Wed Mar 24 2021 - 09:57:26 CDT)
    - Re: how to properly end NAMD replica job on slurm batch system RenÃ© Hafner TUK (Wed Mar 24 2021 - 12:17:49 CDT)
Some Basic queries for FEP and TI Debadrita Basu (Sun Mar 21 2021 - 11:18:50 CDT)
- Re: Some Basic queries for FEP and TI Brian Radak (Sun Mar 21 2021 - 14:41:11 CDT)
  - Re: Some Basic queries for FEP and TI Debadrita Basu (Mon Mar 22 2021 - 06:48:57 CDT)
Compiling namd2 in 2 GPU 2 CPU workstation Suryanarayanan Chandrasekaran (Sat Mar 20 2021 - 04:58:58 CDT)
- Re: Compiling namd2 in 2 GPU 2 CPU workstation Vermaas, Josh (Sat Mar 20 2021 - 18:11:59 CDT)
  - Re: Compiling namd2 in 2 GPU 2 CPU workstation Suryanarayanan Chandrasekaran (Sun Mar 21 2021 - 23:24:45 CDT)
    - Re: Compiling namd2 in 2 GPU 2 CPU workstation Vermaas, Josh (Mon Mar 22 2021 - 08:47:29 CDT)
  - Re: Compiling namd2 in 2 GPU 2 CPU workstation Vermaas, Josh (Tue Mar 23 2021 - 08:00:52 CDT)
Lipid into sphere Ropon-Palacios G. (Thu Mar 18 2021 - 16:25:59 CDT)
- Re: Lipid into sphere Mike McCallum (Thu Mar 18 2021 - 17:13:26 CDT)
  - Re: Lipid into sphere Ropon-Palacios G. (Thu Mar 18 2021 - 17:18:34 CDT)
NAMD QMMM: Electrostatic energy and PMECORRENERGY Alex Balaeff (Thu Mar 18 2021 - 12:17:11 CDT)
Rule of thumb for choosing time step in MD Mi Yang (Tue Mar 16 2021 - 15:12:08 CDT)
- Re: Rule of thumb for choosing time step in MD David Hardy (Tue Mar 16 2021 - 16:23:21 CDT)
AMBER99bsc1 force field for NAMD Almeida-Hernández, Yasser, Dr. (Tue Mar 16 2021 - 05:06:25 CDT)
Lone pair disconnected after minimization Rabiul Gazi (Mon Mar 15 2021 - 04:36:13 CDT)
- Re: Lone pair disconnected after minimization David Hardy (Tue Mar 16 2021 - 17:23:59 CDT)
Add repulsive potential with dummy atom Ropon-Palacios G. (Fri Mar 12 2021 - 14:54:01 CST)
- Re: Add repulsive potential with dummy atom David Hardy (Tue Mar 16 2021 - 13:31:53 CDT)
  - Re: Add repulsive potential with dummy atom ROPÃ“N-PALACIOS G. (Tue Mar 16 2021 - 16:23:22 CDT)
Avoiding unfavorable interactions during Docking with Vina Mi Yang (Fri Mar 12 2021 - 13:05:23 CST)
Ligand concentration Ropon-Palacios G. (Thu Mar 11 2021 - 21:09:31 CST)
Ligand concentration Ropon-Palacios G. (Thu Mar 11 2021 - 20:50:28 CST)
3.0alpha9 CUDA version Michael Von Domaros (Thu Mar 11 2021 - 18:42:23 CST)
- Re: 3.0alpha9 CUDA version Vermaas, Josh (Thu Mar 11 2021 - 19:27:53 CST)
Axis Definition in Metadynamics Sodiq Waheed (Wed Mar 10 2021 - 12:56:17 CST)
- Re: Axis Definition in Metadynamics ROPÃ“N-PALACIOS G. (Thu Mar 11 2021 - 10:21:32 CST)
Lone pair disconnected after minimization Rabiul Gazi (Mon Mar 08 2021 - 03:03:44 CST)
NAMD and VMD on AMAZON instances Ropon-Palacios G. (Sun Mar 07 2021 - 23:33:10 CST)
N-glycosylation bond not view after patching Ropon-Palacios G. (Sun Mar 07 2021 - 17:15:26 CST)
- Re: N-glycosylation bond not view after patching Gumbart, JC (Sun Mar 07 2021 - 22:15:35 CST)
NAMD3 Alpha7 MultiGPU errors Raman Preet Singh (Sun Mar 07 2021 - 07:01:04 CST)
Applying an external field to the electrostatic potential map soumadwip ghosh (Sat Mar 06 2021 - 02:13:16 CST)
- Re: Applying an external field to the electrostatic potential map David Hardy (Tue Mar 16 2021 - 13:40:29 CDT)
(no subject) soumadwip ghosh (Sat Mar 06 2021 - 02:12:11 CST)
Placed random molecules into Box Ropon-Palacios G. (Fri Mar 05 2021 - 16:05:22 CST)
- Re: Placed random molecules into Box Bennion, Brian (Fri Mar 05 2021 - 17:29:37 CST)
simulations under a periodic electric field - possible bug Oleksii Zdorevskyi (Fri Mar 05 2021 - 11:11:29 CST)
Re: Compile NAMD with AMD GPU Vermaas, Josh (Wed Mar 03 2021 - 15:33:43 CST)
Compile NAMD with AMD GPU Ropon-Palacios G. (Wed Mar 03 2021 - 15:12:23 CST)
Negative current in open pore simulation soumadwip ghosh (Wed Mar 03 2021 - 00:32:20 CST)
Dual topology questions Randall Hall (Mon Mar 01 2021 - 20:01:52 CST)
NAMD 3.0 FEP Atoms moving too fast error Michael Joseph Robertson (Fri Feb 26 2021 - 04:22:32 CST)
Re: CHARMM Parameter question Ramon Mendoza Uriarte (Thu Feb 25 2021 - 15:26:33 CST)
Namd-3 alpha 7 error Dr. Eddie (Tue Feb 23 2021 - 11:49:01 CST)
- Re: Namd-3 alpha 7 error David Hardy (Wed Feb 24 2021 - 13:28:23 CST)
  - Re: Namd-3 alpha 7 error Bassam Haddad (Wed Feb 24 2021 - 13:42:32 CST)
    - Re: Namd-3 alpha 7 error Dr. Eddie (Wed Feb 24 2021 - 14:25:16 CST)
  - Re: Namd-3 alpha 7 error Dr. Eddie (Wed Feb 24 2021 - 14:38:26 CST)
Small molecule simulation error NAMD Chathuranga Siriwardhana (Mon Feb 22 2021 - 17:28:35 CST)
- Re: Small molecule simulation error NAMD Jeff Comer (Mon Feb 22 2021 - 17:34:17 CST)
NAMD3 multiGPU: invalid device function error Lorenzo Casalino (Fri Feb 19 2021 - 21:24:19 CST)
- Re: NAMD3 multiGPU: invalid device function error David Hardy (Mon Feb 22 2021 - 16:26:01 CST)
  - Re: NAMD3 multiGPU: invalid device function error David Hardy (Mon Feb 22 2021 - 17:56:32 CST)
  - Re: NAMD3 multiGPU: invalid device function error David Hardy (Mon Feb 22 2021 - 18:35:35 CST)
Error in calculation dihedral angle jiali wang (Fri Feb 12 2021 - 23:54:43 CST)
- Re: Error in calculation dihedral angle Peter Freddolino (Sat Feb 13 2021 - 18:40:08 CST)
  - Re: [External Email] Re: Error in calculation dihedral angle Jiali Wang (Sat Feb 13 2021 - 22:06:38 CST)
    - Re: [External Email] Re: Error in calculation dihedral angle Peter Freddolino (Sat Feb 13 2021 - 22:29:03 CST)
    - Re: [External Email] Re: Error in calculation dihedral angle jiali wang (Sat Feb 13 2021 - 22:33:16 CST)
Problem with running NAMD config file Tiglath Moradkhan (Wed Feb 10 2021 - 19:01:22 CST)
- Re: Problem with running NAMD config file ROPÃ“N-PALACIOS G. (Wed Feb 10 2021 - 22:06:31 CST)
  - Re: Problem with running NAMD config file Tiglath Moradkhan (Thu Feb 11 2021 - 11:28:19 CST)
the centers value in colvar.in file for binding free energy (BFEE) M. A (Fri Feb 05 2021 - 05:26:01 CST)
Issue about replica exchange molecular dynamics è¾›å¿—å®� (Thu Feb 04 2021 - 06:04:53 CST)
Mail about error in namd Vidhya Sankar (Thu Feb 04 2021 - 02:21:28 CST)
NAMD3 Multiple Instances Raman Preet Singh (Wed Feb 03 2021 - 11:50:04 CST)
- Re: NAMD3 Multiple Instances David Hardy (Wed Feb 03 2021 - 14:37:58 CST)
Dealing with lone pairs Seke Keretsu (Wed Feb 03 2021 - 02:51:29 CST)
- RE: Dealing with lone pairs Pang, Yui Tik (Wed Feb 03 2021 - 09:39:01 CST)
- Re: Dealing with lone pairs David Hardy (Wed Feb 03 2021 - 14:31:29 CST)
Re: NAMD CUDA Vermaas, Josh (Mon Feb 01 2021 - 14:12:51 CST)
- Re: NAMD CUDA Brian Radak (Mon Feb 01 2021 - 15:11:43 CST)
  - Re: NAMD CUDA David Hardy (Tue Feb 02 2021 - 18:51:41 CST)
NAMD CUDA Seibold, Steve Allan (Mon Feb 01 2021 - 13:50:11 CST)
- Re: NAMD CUDA Prince, Chandler (Mon Feb 01 2021 - 15:32:51 CST)
  - Re: NAMD CUDA Renfro, Michael (Mon Feb 01 2021 - 16:17:09 CST)
Convert mmCIF to PDB Ropon-Palacios G. (Mon Feb 01 2021 - 12:02:56 CST)
output results to phenix Ming Sun (Mon Feb 01 2021 - 11:26:59 CST)
- Re: output results to phenix Ropon-Palacios G. (Mon Feb 01 2021 - 12:04:27 CST)
Problem with FEP simulations Luba Simhaev (Mon Feb 01 2021 - 02:48:14 CST)
- Re: Problem with FEP simulations David Hardy (Tue Feb 02 2021 - 18:43:57 CST)
Dealing with lone pairs (LP) during simulation Seke Keretsu (Sat Jan 30 2021 - 01:05:09 CST)
- RE: Dealing with lone pairs (LP) during simulation Pang, Yui Tik (Sat Jan 30 2021 - 11:19:21 CST)
Re: Improve performance Vermaas, Josh (Thu Jan 28 2021 - 18:45:52 CST)
- Re: Improve performance Ropon-Palacios G. (Thu Jan 28 2021 - 19:21:33 CST)
  - Re: Improve performance David Hardy (Tue Feb 02 2021 - 18:31:51 CST)
    - Re: Improve performance Ming Sun (Mon Feb 15 2021 - 07:15:00 CST)
    - Re: Improve performance David Hardy (Mon Feb 15 2021 - 18:25:41 CST)
Improve performance Ropon-Palacios G. (Thu Jan 28 2021 - 18:08:39 CST)
Implementing decaying potential (non-linear potential) Athreya, Nagendra Bala Murali (Thu Jan 28 2021 - 14:14:26 CST)
- Re: Implementing decaying potential (non-linear potential) Giacomo Fiorin (Thu Jan 28 2021 - 14:20:55 CST)
  - Re: Implementing decaying potential (non-linear potential) Athreya, Nagendra Bala Murali (Thu Jun 17 2021 - 11:28:43 CDT)
Namd can not be launched for umbrella sample è¾›å¿—å®� (Thu Jan 28 2021 - 05:41:53 CST)
- Re: Namd can not be launched for umbrella sample Victor Kwan (Thu Jan 28 2021 - 10:35:45 CST)
  - Re:Re: Namd can not be launched for umbrella sample è¾›å¿—å®� (Thu Jan 28 2021 - 20:42:33 CST)
    - Re: Re:Re: Namd can not be launched for umbrella sample David Hardy (Tue Feb 02 2021 - 18:35:14 CST)
Multiple replica WTM-eABF simulations interrupted during replica sharing step Abhishek Acharya (Tue Jan 26 2021 - 04:48:33 CST)
Protein RMSF in replica exchange simulations Victor Zhao (Mon Jan 25 2021 - 15:50:03 CST)
- Re: Protein RMSF in replica exchange simulations Brian Radak (Mon Jan 25 2021 - 16:22:39 CST)
  - Re: Protein RMSF in replica exchange simulations Victor Zhao (Mon Jan 25 2021 - 16:26:23 CST)
    - Re: Protein RMSF in replica exchange simulations Brian Radak (Tue Jan 26 2021 - 12:01:44 CST)
Supervised MD using NAMD Dr. Eddie (Mon Jan 25 2021 - 07:27:32 CST)
- Re: Supervised MD using NAMD Seke Keretsu (Mon Jan 25 2021 - 07:39:55 CST)
NAMD speed and Scaling raghav singh (Mon Jan 25 2021 - 06:02:52 CST)
- Re: NAMD speed and Scaling Giacomo Fiorin (Thu Jan 28 2021 - 19:01:54 CST)
Infrared spectrum prediction Raman Preet Singh (Mon Jan 18 2021 - 12:21:23 CST)
- Re: Infrared spectrum prediction Raman Preet Singh (Fri Feb 12 2021 - 04:34:16 CST)
Maximum and minimum box size Raman Preet Singh (Mon Jan 18 2021 - 12:16:42 CST)
- Re: Maximum and minimum box size Raman Preet Singh (Fri Feb 12 2021 - 04:35:31 CST)
  - Re: Re: Maximum and minimum box size David Hardy (Mon Feb 15 2021 - 18:09:20 CST)
NAMD QMMM Scheme nikolaev_at_spbau.ru (Sun Jan 17 2021 - 11:20:54 CST)
- Re: NAMD QMMM Scheme Rafael Bernardi (Sun Jan 17 2021 - 15:23:32 CST)
Judging Convergence on Free Energy Calculations Ethan Croitoru (Fri Jan 15 2021 - 13:45:40 CST)
- Re: Judging Convergence on Free Energy Calculations Josh Vermaas (Fri Jan 15 2021 - 14:13:13 CST)
FATAL ERROR: patch has 127043 atoms, maximum allowed is 65535 Paula Mihaljevic-Juric (Fri Jan 15 2021 - 11:51:37 CST)
NAMD qm/mm: QM charge not integer Chunli Yan (Thu Jan 14 2021 - 11:58:24 CST)
- Re: NAMD qm/mm: QM charge not integer Rafael Bernardi (Thu Jan 14 2021 - 13:39:03 CST)
Problems Building Circular DNA Sebastian S (Mon Jan 11 2021 - 19:42:36 CST)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Thu Jan 07 2021 - 21:56:25 CST)
An running issue in eABF-replica calculations hua hao (Mon Jan 04 2021 - 10:59:56 CST)
- Re: An running issue in eABF-replica calculations RenÃ© Hafner TUK (Mon Mar 01 2021 - 02:28:52 CST)
  - Re: An running issue in eABF-replica calculations hua hao (Mon Mar 01 2021 - 06:22:02 CST)
- Re: An running issue in eABF-replica calculations Abhishek Acharya (Mon Mar 01 2021 - 06:50:20 CST)
  - Re: An running issue in eABF-replica calculations hua hao (Mon Mar 01 2021 - 09:21:29 CST)
namdEnergy empy output file Khoualdi Asma Feriel (Thu Dec 31 2020 - 22:29:18 CST)
- Re: namdEnergy empy output file Peter Freddolino (Fri Jan 01 2021 - 00:24:00 CST)
FEP calculations - membrane protein Luba Simhaev (Thu Dec 31 2020 - 02:45:38 CST)
namdEnergy execution issue -path for namd2 in server Khoualdi Asma Feriel (Wed Dec 30 2020 - 23:23:08 CST)
- Re: namdEnergy execution issue -path for namd2 in server Pratik Narain Srivastava (Thu Dec 31 2020 - 00:17:02 CST)
about geometrical restrain protein on membrane Liqun Zhang (Wed Dec 30 2020 - 21:30:37 CST)
- Re: about geometrical restrain protein on membrane vermaasj (Thu Dec 31 2020 - 09:06:35 CST)
  - Re: about geometrical restrain protein on membrane Liqun Zhang (Thu Dec 31 2020 - 12:04:59 CST)
[NAMD] Example of submission script on Comet/Stampede GPUs Sebastian S (Mon Dec 28 2020 - 12:58:27 CST)
Force Field Parametrization Ramon Mendoza Uriarte (Sun Dec 27 2020 - 19:08:44 CST)
Charmm hybrid topology ROPÃ“N-PALACIOS G. (Sat Dec 26 2020 - 15:32:44 CST)
Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Thu Dec 24 2020 - 13:02:23 CST)
- Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Peter Freddolino (Mon Dec 28 2020 - 23:44:34 CST)
  - Re: Ambiguity among number of residues as counted in VMD and PyMol for RMSF Mi Yang (Wed Dec 30 2020 - 01:27:03 CST)
Question about Radius of hexagon; Seke Keretsu (Thu Dec 24 2020 - 00:33:17 CST)
- Re: Question about Radius of hexagon; Ramon Mendoza Uriarte (Thu Dec 24 2020 - 13:54:06 CST)
Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 14:39:15 CST)
- Re: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Gumbart, JC (Tue Dec 22 2020 - 20:43:36 CST)
  - Re: Query regarding 'Protein:ligand Standard Binding Free Energies' tutorial Faisal, H M Nasrullah (Tue Dec 22 2020 - 20:52:34 CST)
SMD on Intermembrane Helices Ethan Croitoru (Tue Dec 22 2020 - 11:15:45 CST)
- Re: SMD on Intermembrane Helices Ashkan Shekaari (Tue Dec 22 2020 - 11:30:54 CST)
- Re: SMD on Intermembrane Helices Ashkan Shekaari (Tue Dec 22 2020 - 11:32:32 CST)
- Re: SMD on Intermembrane Helices Bassam Haddad (Tue Dec 22 2020 - 11:36:36 CST)
  - Re: SMD on Intermembrane Helices Gumbart, JC (Tue Dec 22 2020 - 20:45:09 CST)
    - Re: SMD on Intermembrane Helices Alex Balaeff (Tue Dec 22 2020 - 20:57:43 CST)
FATAL ERROR: can't read "boxtype" Seke Keretsu (Sun Dec 20 2020 - 20:24:37 CST)
- Re: FATAL ERROR: can't read "boxtype" Bassam Haddad (Tue Dec 22 2020 - 11:31:23 CST)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Mi Yang (Sat Dec 19 2020 - 08:07:11 CST)
- Re: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Roshan Shrestha (Sat Dec 19 2020 - 08:12:30 CST)
  - Re: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Mi Yang (Thu Dec 24 2020 - 02:44:32 CST)
    - Re: ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on patch 42 pe 18). Ashkan Shekaari (Thu Dec 24 2020 - 03:31:57 CST)
path CV Stefano Guglielmo (Fri Dec 18 2020 - 08:48:27 CST)
- Re: path CV Giacomo Fiorin (Fri Dec 18 2020 - 10:35:30 CST)
  - Re: path CV Stefano Guglielmo (Fri Dec 18 2020 - 11:22:05 CST)
    - Re: path CV JÃ©rÃ´me HÃ©nin (Tue Dec 29 2020 - 10:00:16 CST)
    - Re: path CV Stefano Guglielmo (Thu Jan 28 2021 - 02:11:13 CST)
Assessing total time of run in NAMD Mi Yang (Thu Dec 17 2020 - 12:50:33 CST)
- Re: Assessing total time of run in NAMD Ingrid Bernardes Santana Martins (Thu Dec 17 2020 - 13:18:23 CST)
  - Re: Assessing total time of run in NAMD Mi Yang (Fri Dec 18 2020 - 07:38:23 CST)
    - Re: Assessing total time of run in NAMD Josh Vermaas (Fri Dec 18 2020 - 07:52:09 CST)
Force field for Li-ion batteries electrolytes based on ionic liquids Mauro Sgroi (Thu Dec 17 2020 - 03:46:32 CST)
Installation with tcl Arturo Fernandez (Wed Dec 16 2020 - 16:22:33 CST)
- Re: Installation with tcl Josh Vermaas (Wed Dec 16 2020 - 16:50:53 CST)
Water wrapping in the QMMM simulations Alex Balaeff (Mon Dec 14 2020 - 17:27:11 CST)
- Re: Water wrapping in the QMMM simulations Marcelo C. R. Melo (Mon Dec 14 2020 - 18:53:57 CST)
  - Re: Water wrapping in the QMMM simulations Alex Balaeff (Mon Dec 14 2020 - 20:13:27 CST)
I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes Prince, Chandler (Mon Dec 14 2020 - 08:20:48 CST)
- Re: I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes Giacomo Fiorin (Mon Dec 14 2020 - 08:35:16 CST)
  - Re: I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes Prince, Chandler (Mon Dec 14 2020 - 11:24:57 CST)
NAMD QM/MM multi nodes performance bad Chunli Yan (Sun Dec 13 2020 - 20:47:15 CST)
- Re: NAMD QM/MM multi nodes performance bad Josh Vermaas (Sun Dec 13 2020 - 21:53:31 CST)
  - Re: NAMD QM/MM multi nodes performance bad Chunli Yan (Sun Dec 13 2020 - 22:21:52 CST)
Question Colvar o tclforces ROPÃ“N-PALACIOS G. (Sat Dec 12 2020 - 13:15:23 CST)
- Re: Question Colvar o tclforces JÃ©rÃ´me HÃ©nin (Sun Dec 13 2020 - 04:14:27 CST)
  - Re: Question Colvar o tclforces JÃ©rÃ´me HÃ©nin (Mon Dec 14 2020 - 09:42:23 CST)
  - Re: Question Colvar o tclforces ROPÃ“N-PALACIOS G. (Fri Dec 18 2020 - 17:31:34 CST)
Centre of mass distance in ABF Aashish Bhatt (Sat Dec 12 2020 - 02:15:46 CST)
- Re: Centre of mass distance in ABF Giacomo Fiorin (Sat Dec 12 2020 - 09:17:32 CST)
  - Re: Centre of mass distance in ABF Giacomo Fiorin (Thu Dec 17 2020 - 08:38:08 CST)
  - Re: Centre of mass distance in ABF Giacomo Fiorin (Thu Dec 17 2020 - 09:03:45 CST)
    - Re: Centre of mass distance in ABF Aashish Bhatt (Thu Dec 17 2020 - 23:07:59 CST)
About the well-tempered metadynamics convergence.. zeynab hosseini (Thu Dec 10 2020 - 12:49:14 CST)
- Re: About the well-tempered metadynamics convergence.. zeynab hosseini (Thu Dec 10 2020 - 13:01:48 CST)
- Re: About the well-tempered metadynamics convergence.. Giacomo Fiorin (Thu Dec 10 2020 - 13:36:44 CST)
NAMD3: how to get the best performance in one gpu node? Siyoung Kim (Wed Dec 09 2020 - 03:00:02 CST)
- Re: NAMD3: how to get the best performance in one gpu node? vermaasj (Wed Dec 09 2020 - 10:18:41 CST)
Fep setup membrane protein-Drug complex ROPÃ“N-PALACIOS G. (Tue Dec 08 2020 - 13:20:41 CST)
namd QM/MM on oak ridge ANDES cluster Chunli Yan (Sun Dec 06 2020 - 19:14:06 CST)
- Re: namd QM/MM on oak ridge ANDES cluster Marcelo C. R. Melo (Thu Dec 10 2020 - 11:06:02 CST)
Free Energy Pertubation simulation set-up alli suliat (Sun Dec 06 2020 - 18:19:23 CST)
- Re: Free Energy Pertubation simulation set-up ROPÃ“N-PALACIOS G. (Sun Dec 06 2020 - 23:33:51 CST)
NAMD3 segfault while writing restart files David Sept (Sat Dec 05 2020 - 11:09:55 CST)
Membrana-protein-lig protocol ROPÃ“N-PALACIOS G. (Fri Dec 04 2020 - 12:42:24 CST)
Hydrogen Mass Repartitioning McGuire, Kelly (Thu Dec 03 2020 - 21:04:50 CST)
- RE: Hydrogen Mass Repartitioning Mohammed umar Sheriff (Thu Dec 03 2020 - 21:35:10 CST)
  - Re: Hydrogen Mass Repartitioning Gumbart, JC (Thu Dec 03 2020 - 21:57:23 CST)
CPU vs GPU Question McGuire, Kelly (Wed Dec 02 2020 - 16:51:37 CST)
- Re: CPU vs GPU Question Bennion, Brian (Wed Dec 02 2020 - 17:05:50 CST)
  - Re: CPU vs GPU Question McGuire, Kelly (Thu Dec 03 2020 - 21:05:05 CST)
  - Re: CPU vs GPU Question McGuire, Kelly (Wed Dec 09 2020 - 01:14:47 CST)
- Re: CPU vs GPU Question Mohammed umar Sheriff (Sat Dec 05 2020 - 05:33:54 CST)
Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 13:43:17 CST)
- Re: Termination between Minimization to Equilibration Ramon Mendoza Uriarte (Wed Dec 02 2020 - 18:11:37 CST)
  - Re: Re: Termination between Minimization to Equilibration Peter Freddolino (Wed Dec 02 2020 - 19:35:52 CST)
Advice for Protein Mutation FEP Calculations Matthew Guberman-Pfeffer (Tue Dec 01 2020 - 10:27:43 CST)
- Re: Advice for Protein Mutation FEP Calculations JÃ©rÃ´me HÃ©nin (Tue Dec 01 2020 - 13:30:54 CST)
NamdEnergy Nonbonded H-bonds Francesco Pietra (Mon Nov 30 2020 - 11:06:52 CST)
- Re: NamdEnergy Nonbonded H-bonds Peter Freddolino (Mon Nov 30 2020 - 19:28:16 CST)
not getting NAMD multicopy simulation started RenÃ© Hafner TUK (Mon Nov 23 2020 - 07:22:36 CST)
- Re: not getting NAMD multicopy simulation started RenÃ© Hafner TUK (Wed Nov 25 2020 - 07:45:33 CST)
  - Re: not getting NAMD multicopy simulation started Josh Vermaas (Wed Nov 25 2020 - 10:11:58 CST)
Implicit MD is slower than explcit MD! Krishna Vkm (Mon Nov 23 2020 - 05:18:51 CST)
- Re: Implicit MD is slower than explcit MD! Aravinda Munasinghe (Sun Nov 29 2020 - 09:01:30 CST)
Cavernous Depressions in Water Box Oscar Bastidas (Sat Nov 21 2020 - 19:22:14 CST)
- Re: Cavernous Depressions in Water Box Peter Freddolino (Sat Nov 21 2020 - 21:14:01 CST)
  - Re: Cavernous Depressions in Water Box Oscar Bastidas (Thu Dec 31 2020 - 15:26:31 CST)
- Re: Cavernous Depressions in Water Box Alex Balaeff (Sun Nov 22 2020 - 12:21:45 CST)
regarding constant PH simulation zahra nabavi (Thu Nov 19 2020 - 21:07:35 CST)
- Re: regarding constant PH simulation Jeff Comer (Thu Nov 19 2020 - 21:25:24 CST)
  - Re: regarding constant PH simulation Brian Radak (Fri Nov 20 2020 - 07:31:12 CST)
    - Re: regarding constant PH simulation zahra nabavi (Fri Nov 20 2020 - 11:15:36 CST)
Restarting QMMM Francesco Pietra (Thu Nov 19 2020 - 05:13:41 CST)
- Re: Restarting QMMM Marcelo C. R. Melo (Wed Dec 02 2020 - 14:44:45 CST)
  - Re: Restarting QMMM Francesco Pietra (Thu Dec 03 2020 - 04:42:26 CST)
performing SMD in Z using colvar module RopÃ³n-Palacios G. (Mon Nov 16 2020 - 16:16:33 CST)
- Re: performing SMD in Z using colvar module JÃ©rÃ´me HÃ©nin (Tue Nov 17 2020 - 03:50:14 CST)
  - Re: performing SMD in Z using colvar module JÃ©rÃ´me HÃ©nin (Wed Nov 18 2020 - 07:15:22 CST)
Exit code 127 with QMMM Francesco Pietra (Mon Nov 16 2020 - 10:58:30 CST)
- Re: Exit code 127 with QMMM Marcelo C. R. Melo (Mon Nov 16 2020 - 11:26:49 CST)
  - Re: Exit code 127 with QMMM Francesco Pietra (Tue Nov 17 2020 - 03:25:07 CST)
    - Re: Exit code 127 with QMMM Marcelo C. R. Melo (Tue Nov 17 2020 - 12:18:36 CST)
    - Re: Exit code 127 with QMMM Francesco Pietra (Tue Nov 17 2020 - 14:13:29 CST)
NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Seke Keretsu (Mon Nov 16 2020 - 01:55:06 CST)
- Re: NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Josh Vermaas (Mon Nov 16 2020 - 10:01:54 CST)
  - Re: NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Josh Vermaas (Mon Nov 16 2020 - 11:13:36 CST)
    - Re: NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system Peter Freddolino (Mon Nov 16 2020 - 11:40:28 CST)
Adding bias potential Peter Rosenquist (Thu Nov 12 2020 - 15:00:38 CST)
- Re: Adding bias potential Pang, Yui Tik (Thu Nov 12 2020 - 15:25:58 CST)
- IMD simulation RopÃ³n-Palacios G. (Thu Nov 12 2020 - 19:03:23 CST)
Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Wed Nov 11 2020 - 13:04:29 CST)
- Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. JÃ©rÃ´me HÃ©nin (Wed Nov 11 2020 - 13:53:36 CST)
  - Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Wed Nov 11 2020 - 16:13:39 CST)
    - Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. JÃ©rÃ´me HÃ©nin (Mon Nov 16 2020 - 14:10:50 CST)
    - Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator. Abhishek Acharya (Thu Nov 19 2020 - 00:02:49 CST)
FEP/Î»-REMD Simulation error Alao, John-Paul (Mon Nov 09 2020 - 11:01:26 CST)
- Re: FEP/Î»-REMD Simulation error ROPÃ“N-PALACIOS G. (Mon Nov 09 2020 - 12:51:31 CST)
  - Re: FEP/Î»-REMD Simulation error Alao, John-Paul (Mon Nov 09 2020 - 13:00:39 CST)
    - Re: FEP/Î»-REMD Simulation error RopÃ³n-Palacios G. (Mon Nov 09 2020 - 14:30:01 CST)
psf generation for multiple trehalose molecules Ritu Arora (Sun Nov 08 2020 - 18:24:15 CST)
- Re: psf generation for multiple trehalose molecules Josh Vermaas (Sun Nov 08 2020 - 20:13:20 CST)
  - Re: psf generation for multiple trehalose molecules Ritu Arora (Sun Nov 08 2020 - 21:46:15 CST)
    - Re: psf generation for multiple trehalose molecules Peter Freddolino (Mon Nov 09 2020 - 00:08:01 CST)
    - Re: psf generation for multiple trehalose molecules Ritu Arora (Mon Nov 09 2020 - 04:12:07 CST)
  - Re: psf generation for multiple trehalose molecules Ritu Arora (Mon Nov 09 2020 - 10:33:55 CST)
Setting up QM-MM with homotrimer Francesco Pietra (Thu Nov 05 2020 - 10:52:27 CST)
- Re: Setting up QM-MM with homotrimer Francesco Pietra (Mon Nov 16 2020 - 11:54:04 CST)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Wed Nov 04 2020 - 10:47:22 CST)
Rmsd calculation Asmi Mahmood (Tue Nov 03 2020 - 00:22:54 CST)
- Re: Rmsd calculation Atanu Maity (Tue Nov 03 2020 - 19:42:33 CST)
  - Re: Rmsd calculation Asmi Mahmood (Wed Nov 04 2020 - 04:12:00 CST)
rmsd Asmi Mahmood (Mon Nov 02 2020 - 04:41:35 CST)
rmsd colvar Stefano Guglielmo (Sun Nov 01 2020 - 10:17:10 CST)
- Re: rmsd colvar Giacomo Fiorin (Mon Nov 02 2020 - 08:57:31 CST)
NPT then NVT simulation in a single config file for water box? Tanooj Shah (Fri Oct 30 2020 - 21:52:19 CDT)
- Re: NPT then NVT simulation in a single config file for water box? Tanooj Shah (Sun Nov 01 2020 - 09:36:15 CST)
  - Re: NPT then NVT simulation in a single config file for water box? Hemanth Haridas (Tue Nov 03 2020 - 00:27:18 CST)
restart file Constantin Gunkel (Fri Oct 30 2020 - 09:45:17 CDT)
- Re: restart file Peter Freddolino (Fri Oct 30 2020 - 10:43:03 CDT)
Problem Constantin Gunkel (Wed Oct 28 2020 - 20:15:43 CDT)
- Re: Problem Peter Freddolino (Thu Oct 29 2020 - 06:57:17 CDT)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Wed Oct 28 2020 - 09:44:24 CDT)
- Re: model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Thu Oct 29 2020 - 17:02:44 CDT)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Tue Oct 27 2020 - 10:04:49 CDT)
Compile NAMD with PLUMED Jiali Wang (Mon Oct 26 2020 - 22:15:28 CDT)
Can Namd 2.14 and genpsf 2.0 process halogen bonds? Nan Li (Mon Oct 26 2020 - 17:15:06 CDT)
- RE: Can Namd 2.14 and genpsf 2.0 process halogen bonds? Pang, Yui Tik (Tue Oct 27 2020 - 13:00:14 CDT)
(no subject) Mersch, Kacey (Mon Oct 26 2020 - 16:33:00 CDT)
- Re: Josh Vermaas (Mon Oct 26 2020 - 18:21:20 CDT)
- Re: Jeff Comer (Mon Oct 26 2020 - 18:37:05 CDT)
- Re: Peter Freddolino (Mon Oct 26 2020 - 19:16:57 CDT)
model with TIP4 water minimization getting crashed every time Faisal, H M Nasrullah (Mon Oct 26 2020 - 12:50:33 CDT)
Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Mon Oct 26 2020 - 07:33:11 CDT)
- Re: Running multiple walker metadynamics replicas as a bundle Josh Vermaas (Mon Oct 26 2020 - 11:04:02 CDT)
  - Re: Running multiple walker metadynamics replicas as a bundle Giacomo Fiorin (Mon Oct 26 2020 - 13:49:10 CDT)
    - Re: Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Wed Oct 28 2020 - 04:01:19 CDT)
    - Re: Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Wed Oct 28 2020 - 06:18:55 CDT)
  - Re: Running multiple walker metadynamics replicas as a bundle zeynab hosseini (Wed Oct 28 2020 - 04:02:35 CDT)
Repulsive wall potential or spherical boundry conditions Almeida-Hernández, Yasser, Dr. (Fri Oct 23 2020 - 05:13:55 CDT)
- Re: Repulsive wall potential or spherical boundry conditions Giacomo Fiorin (Fri Oct 23 2020 - 10:31:17 CDT)
  - Re: Repulsive wall potential or spherical boundry conditions Almeida-Hernández, Yasser, Dr. (Fri Oct 23 2020 - 12:58:25 CDT)
How to Selectively Scale Interactions Matthew Guberman-Pfeffer (Thu Oct 22 2020 - 23:30:47 CDT)
Velocity MAP calculation in VMD Abhijit Gogoi (Wed Oct 21 2020 - 03:59:13 CDT)
Protein:ligand standard binding free energies clarification question Ethan Croitoru (Tue Oct 20 2020 - 21:14:53 CDT)
- Re: Protein:ligand standard binding free energies clarification question JC Gumbart (Tue Oct 20 2020 - 23:33:22 CDT)
NAMD 2.14 fatal error executing tcl script Alsaloum, Matthew (Sun Oct 18 2020 - 21:06:58 CDT)
- Re: NAMD 2.14 fatal error executing tcl script Josh Vermaas (Mon Oct 19 2020 - 14:01:33 CDT)
  - Re: NAMD 2.14 fatal error executing tcl script Alsaloum, Matthew (Tue Oct 20 2020 - 11:10:20 CDT)
well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Fri Oct 16 2020 - 03:44:27 CDT)
- Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Fri Oct 16 2020 - 09:10:26 CDT)
  - Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Mon Oct 19 2020 - 12:36:07 CDT)
    - Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. Giacomo Fiorin (Mon Oct 19 2020 - 13:34:20 CDT)
  - Re: well-tempered metadynamics deforms the water box and the system becomes unstable.. zeynab hosseini (Tue Oct 20 2020 - 15:33:10 CDT)
GPU Acceleration and Drude Simulations Michael Robinson (Fri Oct 16 2020 - 01:23:57 CDT)
MM/QM with namd Asmi Mahmood (Thu Oct 15 2020 - 08:04:32 CDT)
- Re: MM/QM with namd Marcelo C. R. Melo (Thu Oct 15 2020 - 12:02:38 CDT)
  - Re: MM/QM with namd jing liang (Fri Oct 16 2020 - 09:38:48 CDT)
NAMD QM/MM simulations jing liang (Thu Oct 15 2020 - 03:18:48 CDT)
Targeted MD in NAMD 3.0? Smith, Harper E. (Tue Oct 13 2020 - 11:18:03 CDT)
- Re: Targeted MD in NAMD 3.0? JÃ©rÃ´me HÃ©nin (Wed Oct 14 2020 - 08:48:39 CDT)
  - Re: Targeted MD in NAMD 3.0? Giacomo Fiorin (Wed Oct 14 2020 - 09:15:30 CDT)
    - Re: Targeted MD in NAMD 3.0? Josh Vermaas (Wed Oct 14 2020 - 09:28:14 CDT)
A home PC to run NAMD simulations Harish Srinivasan (Sun Oct 11 2020 - 02:02:27 CDT)
- Re: A home PC to run NAMD simulations Adupa Vasista (Sun Oct 11 2020 - 04:13:12 CDT)
  - RE: A home PC to run NAMD simulations Sanjay Hari (Tue Oct 13 2020 - 15:03:07 CDT)
Question about PBC and RMSD alli suliat (Sat Oct 10 2020 - 00:31:11 CDT)
- Re: Question about PBC and RMSD Pratik Narain Srivastava (Sat Oct 10 2020 - 03:22:28 CDT)
Formation of nanoparticle ligand complex Yuvam Bhateja (Fri Oct 09 2020 - 14:09:30 CDT)
Quary resgading Adaptive biasing force Aashish Bhatt (Thu Oct 08 2020 - 08:43:44 CDT)
- Re: Quary resgading Adaptive biasing force Giacomo Fiorin (Thu Oct 08 2020 - 09:36:35 CDT)
Transition State Search BY NAMD è¾›å¿—å®� (Wed Oct 07 2020 - 02:26:58 CDT)
- Re: Transition State Search BY NAMD Pawel Kedzierski (Wed Oct 07 2020 - 02:57:04 CDT)
amber force field divyabharathi korlepara (Tue Oct 06 2020 - 23:51:49 CDT)
COLVARs for Cremer-Pople puckering parameters in NAMD Metadynamics Chythra J N (Tue Oct 06 2020 - 21:57:46 CDT)
- Re: COLVARs for Cremer-Pople puckering parameters in NAMD Metadynamics JÃ©rÃ´me HÃ©nin (Wed Oct 07 2020 - 05:26:59 CDT)
shifting of ions from -z to +z in a single frame(1ps) Basanta Acharya (Tue Oct 06 2020 - 21:54:07 CDT)
Ligand coated Silver Nanoparticle. Yuvam Bhateja (Tue Oct 06 2020 - 11:19:02 CDT)
CHARMM36 to Drude conversion for NAMD Almeida-Hernández, Yasser, Dr. (Tue Oct 06 2020 - 03:37:32 CDT)
Optimum time for md run in i3 laptop achchirangeebi (Tue Oct 06 2020 - 01:30:55 CDT)
- Re: Optimum time for md run in i3 laptop Pratik Narain Srivastava (Tue Oct 06 2020 - 01:35:06 CDT)
NAMD doesn't use my CUDA enabled GPU Rimon Riju (Tue Oct 06 2020 - 01:17:45 CDT)
- Re: NAMD doesn't use my CUDA enabled GPU Pratik Narain Srivastava (Tue Oct 06 2020 - 01:36:01 CDT)
Regarding "lossiness" of namd on GPUs Bassam Haddad (Mon Oct 05 2020 - 16:19:26 CDT)
- Re: Regarding "lossiness" of namd on GPUs Josh Vermaas (Mon Oct 05 2020 - 16:26:29 CDT)
- Re: Regarding "lossiness" of namd on GPUs Victor Kwan (Mon Oct 05 2020 - 16:26:54 CDT)
  - Re: Regarding "lossiness" of namd on GPUs Bassam Haddad (Mon Oct 05 2020 - 16:30:50 CDT)
psf generation divyabharathi korlepara (Mon Oct 05 2020 - 10:13:35 CDT)
- Re: psf generation Sanjay Hari (Mon Oct 05 2020 - 10:31:16 CDT)
- Re: psf generation Josh Vermaas (Mon Oct 05 2020 - 11:51:24 CDT)
- Re: psf generation Ashkan Shekaari (Mon Oct 05 2020 - 13:52:43 CDT)
  - Re: psf generation divyabharathi korlepara (Tue Oct 06 2020 - 00:45:24 CDT)
    - Re: psf generation Pratik Narain Srivastava (Tue Oct 06 2020 - 01:37:04 CDT)
Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:08:48 CDT)
- Re: Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:35:52 CDT)
  - Re: Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:46:46 CDT)
How to determine the residue of qmLSSRef in QwikMD? è¾›å¿—å®� (Sun Oct 04 2020 - 20:28:28 CDT)
Incorrect restarting velocities Kodituwakku,Dimuthu Nirmani (Fri Oct 02 2020 - 09:53:02 CDT)
QwikMD--ERROR) Unable to ascertain relative endianness of remote machine è¾›å¿—å®� (Fri Oct 02 2020 - 03:18:39 CDT)
- Re: QwikMD--ERROR) Unable to ascertain relative endianness of remote machine Victor Kwan (Fri Oct 02 2020 - 19:23:36 CDT)
  - Re:Re: QwikMD--ERROR) Unable to ascertain relative endianness of remote machine è¾›å¿—å®� (Fri Oct 02 2020 - 20:47:05 CDT)
  - Re:Re: QwikMD--ERROR) Unable to ascertain relative endianness of remote machine è¾›å¿—å®� (Sat Oct 03 2020 - 07:19:56 CDT)
TMD questions - refined Nadia Elghobashi-Meinhardt (Thu Oct 01 2020 - 08:59:18 CDT)
- Re: TMD questions - refined Ashkan Shekaari (Thu Oct 01 2020 - 09:14:33 CDT)
  - Re: TMD questions - refined Nadia Elghobashi-Meinhardt (Fri Oct 02 2020 - 03:54:52 CDT)
renumbering and rewriting a trajectory Kodituwakku,Dimuthu Nirmani (Wed Sep 30 2020 - 10:30:25 CDT)
- Re: renumbering and rewriting a trajectory RenÃ© Hafner TUK (Wed Sep 30 2020 - 10:41:02 CDT)
  - Re: renumbering and rewriting a trajectory Kodituwakku,Dimuthu Nirmani (Sat Oct 03 2020 - 22:12:05 CDT)
    - Re: renumbering and rewriting a trajectory RenÃ© Hafner TUK (Mon Oct 05 2020 - 10:30:54 CDT)
- Re: renumbering and rewriting a trajectory Kodituwakku,Dimuthu Nirmani (Fri Oct 02 2020 - 09:28:13 CDT)
REUS Ashkan Shekaari (Mon Sep 28 2020 - 11:37:29 CDT)
- Re: REUS zeynab hosseini (Fri Oct 09 2020 - 13:51:32 CDT)
WHAM Ashkan Shekaari (Mon Sep 28 2020 - 08:40:02 CDT)
TMD config parameters Nadia Elghobashi-Meinhardt (Fri Sep 25 2020 - 02:48:06 CDT)
VMD nc file problem Seibold, Steve Allan (Thu Sep 24 2020 - 09:20:51 CDT)
NAMD trajectory with MMPBSA.py Asmi Mahmood (Wed Sep 23 2020 - 09:36:52 CDT)
- Re: NAMD trajectory with MMPBSA.py I. Camps (Wed Sep 23 2020 - 09:54:08 CDT)
REMD Problem Anup Prasad (Wed Sep 23 2020 - 05:47:08 CDT)
Getting high performance on multi-copy (replica) GPU simulations Victor Zhao (Tue Sep 22 2020 - 11:12:58 CDT)
- Re: Getting high performance on multi-copy (replica) GPU simulations Josh Vermaas (Tue Sep 22 2020 - 13:04:26 CDT)
  - Re: Getting high performance on multi-copy (replica) GPU simulations Victor Zhao (Wed Sep 23 2020 - 00:04:27 CDT)
Regarding to the parameters of QwikMD è¾›å¿—å®� (Tue Sep 22 2020 - 09:42:12 CDT)
Error running command for QM forces calculation è¾›å¿—å®� (Mon Sep 21 2020 - 01:21:20 CDT)
Farnesylated Cysteine Xu, Shenyuan (Sun Sep 20 2020 - 10:55:46 CDT)
- Re: Farnesylated Cysteine Josh Vermaas (Mon Sep 21 2020 - 11:23:35 CDT)
  - Re: Farnesylated Cysteine Xu, Shenyuan (Wed Sep 23 2020 - 20:39:05 CDT)
namd3 on centos 6 Boyan Bonev (Sat Sep 19 2020 - 07:49:07 CDT)
- Re: namd3 on centos 6 Pratik Narain Srivastava (Sat Sep 19 2020 - 09:04:24 CDT)
  - RE: namd3 on centos 6 Sanjay Hari (Mon Sep 21 2020 - 16:46:36 CDT)
- Re: namd3 on centos 6 Victor Kwan (Sun Sep 20 2020 - 13:07:50 CDT)
(no subject) shyam sharma (Fri Sep 18 2020 - 04:20:27 CDT)
(no subject) shyam sharma (Fri Sep 18 2020 - 03:58:41 CDT)
Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 10:07:35 CDT)
- Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Giacomo Fiorin (Thu Sep 17 2020 - 10:40:50 CDT)
  - Re: Output of harmonic restrains effect in alchemical route of protein-ligand binding free energy calculation Faisal, H M Nasrullah (Thu Sep 17 2020 - 13:20:05 CDT)
Atom outside of the MSM grid in NVT simulation - Semiperiodic boundaries Guna Mandava (Wed Sep 16 2020 - 21:20:28 CDT)
MD simulation of a molecule with a halogen Federico Rui (Wed Sep 16 2020 - 11:22:17 CDT)
simulated annealing Stefano Guglielmo (Wed Sep 16 2020 - 10:53:09 CDT)
Convert solvated CHARMM PDB + PSF to Amber Gianluca Interlandi (Tue Sep 15 2020 - 20:34:44 CDT)
- Re: Convert solvated CHARMM PDB + PSF to Amber Michael Robinson (Wed Sep 16 2020 - 23:08:52 CDT)
  - Re: Convert solvated CHARMM PDB + PSF to Amber Gianluca Interlandi (Thu Sep 17 2020 - 20:00:59 CDT)
    - Re: Convert solvated CHARMM PDB + PSF to Amber Michael Robinson (Fri Sep 18 2020 - 02:22:16 CDT)
Parameters and topology files regarding arsorite(ASO3 - - -) Basanta Acharya (Tue Sep 15 2020 - 07:29:51 CDT)
(no subject) Basanta Acharya (Tue Sep 15 2020 - 07:27:03 CDT)
AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 00:53:42 CDT)
- Re: AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 11:04:16 CDT)
  - Re: Re: AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 12:01:43 CDT)
    - Re: Re: AMBER input and REST2 leads to crash David Hardy (Tue Sep 15 2020 - 12:26:55 CDT)
    - Re: Re: AMBER input and REST2 leads to crash Victor Zhao (Tue Sep 15 2020 - 17:33:54 CDT)
NAN in output of aMD Ritu Arora (Mon Sep 14 2020 - 09:33:03 CDT)
- Re: NAN in output of aMD HEMANTH H (Tue Sep 15 2020 - 00:55:59 CDT)
  - Re: NAN in output of aMD Ritu Arora (Tue Sep 15 2020 - 13:26:11 CDT)
    - Re: NAN in output of aMD Giacomo Fiorin (Wed Sep 16 2020 - 16:25:36 CDT)
    - Re: NAN in output of aMD Ritu Arora (Thu Sep 17 2020 - 10:54:33 CDT)
Hybrid Coarse Grain/ all atom simulation in NAMD Shadi Rahnama (Sun Sep 13 2020 - 14:18:26 CDT)
Post processing NAMD trajectory Kodituwakku,Dimuthu Nirmani (Sun Sep 13 2020 - 13:08:14 CDT)
- Re: Post processing NAMD trajectory Josh Vermaas (Sun Sep 13 2020 - 15:55:57 CDT)
- Re: Post processing NAMD trajectory Josh Vermaas (Sun Sep 13 2020 - 15:56:12 CDT)
- Re: Post processing NAMD trajectory Alex Balaeff (Sun Sep 13 2020 - 21:26:34 CDT)
  - Re: Post processing NAMD trajectory Kodituwakku,Dimuthu Nirmani (Tue Sep 15 2020 - 20:46:39 CDT)
Equilibration of a solvated CNT using C36 zeynab hosseini (Sun Sep 13 2020 - 09:01:52 CDT)
- Re: Equilibration of a solvated CNT using C36 Axel Kohlmeyer (Sun Sep 13 2020 - 13:14:18 CDT)
FATAL ERROR: Error running command for QM forces calculation è¾›å¿—å®� (Sun Sep 13 2020 - 07:52:13 CDT)
toppar_water_ions.str NAMD format for last version of C36 (on July 2020) zeynab hosseini (Tue Sep 01 2020 - 13:29:11 CDT)
- Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) Josh Vermaas (Sat Sep 12 2020 - 16:44:27 CDT)
  - Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) zeynab hosseini (Wed Sep 02 2020 - 07:03:11 CDT)
    - Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) Josh Vermaas (Sun Sep 13 2020 - 10:45:31 CDT)
    - Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020) zeynab hosseini (Sun Sep 13 2020 - 10:47:16 CDT)
ERROR: Atoms moving too fast; simulation has become unstable è¾›å¿—å®� (Wed Sep 09 2020 - 23:03:53 CDT)
- Re: ERROR: Atoms moving too fast; simulation has become unstable Natalia Ostrowska (Thu Sep 10 2020 - 03:40:27 CDT)
  - Re:Re: ERROR: Atoms moving too fast; simulation has become unstable è¾›å¿—å®� (Thu Sep 10 2020 - 04:35:27 CDT)
DRMS Colvar Ethan Croitoru (Wed Sep 09 2020 - 14:25:33 CDT)
- Re: DRMS Colvar Giacomo Fiorin (Wed Sep 09 2020 - 14:55:47 CDT)
Basics of MD Raman Preet Singh (Tue Sep 08 2020 - 05:10:10 CDT)
- Re: Basics of MD Peter Freddolino (Tue Sep 08 2020 - 10:17:37 CDT)
  - Re: Basics of MD JC Gumbart (Tue Sep 08 2020 - 11:46:16 CDT)
    - RE: Basics of MD Lennart Nilsson (Tue Sep 08 2020 - 13:05:28 CDT)
    - Re: Basics of MD JC Gumbart (Tue Sep 08 2020 - 13:51:42 CDT)
How to treat electrostatics in crystal lattice MD simulation Matthew Guberman-Pfeffer (Mon Sep 07 2020 - 07:02:17 CDT)
- Re: How to treat electrostatics in crystal lattice MD simulation Peter Freddolino (Mon Sep 07 2020 - 09:46:13 CDT)
Issue regarding to the speed of QM/MM è¾›å¿—å®� (Mon Sep 07 2020 - 03:40:03 CDT)
- Re: Issue regarding to the speed of QM/MM Marcelo C. R. Melo (Mon Sep 07 2020 - 13:11:07 CDT)
<< Setting the simulation time parameters >> I. Camps (Sat Sep 05 2020 - 13:44:17 CDT)
<< Conformational sampling with NAMD >> I. Camps (Sat Sep 05 2020 - 12:54:13 CDT)
Support for drudeNbthole on CUDA version of NAMD HEMANTH H (Sat Sep 05 2020 - 02:15:51 CDT)
- Re: Support for drudeNbthole on CUDA version of NAMD David Hardy (Tue Sep 15 2020 - 12:06:22 CDT)
  - Re: Support for drudeNbthole on CUDA version of NAMD Dr. Eddie (Mon Oct 04 2021 - 14:33:59 CDT)
xMDFF Error Joey Farrell (Thu Sep 03 2020 - 23:19:47 CDT)
ABF Not Sampling Whole Window Ethan Croitoru (Thu Sep 03 2020 - 18:35:15 CDT)
- Re: ABF Not Sampling Whole Window JÃ©rÃ´me HÃ©nin (Tue Sep 08 2020 - 11:18:32 CDT)
  - Re: ABF Not Sampling Whole Window JÃ©rÃ´me HÃ©nin (Fri Sep 11 2020 - 05:24:34 CDT)
Replica exchange problem Julian David Baquero Contreras (Wed Sep 02 2020 - 13:13:59 CDT)
- Re: Replica exchange problem Josh Vermaas (Wed Sep 02 2020 - 17:10:12 CDT)
  - Re: Replica exchange problem Josh Vermaas (Mon Sep 21 2020 - 15:36:19 CDT)
    - Re: Replica exchange problem Julian David Baquero Contreras (Mon Sep 21 2020 - 16:54:35 CDT)
Colvars Harmonic Bias Force Direction Mortimer Hemmit (Wed Sep 02 2020 - 07:28:03 CDT)
- Re: Colvars Harmonic Bias Force Direction JÃ©rÃ´me HÃ©nin (Wed Sep 02 2020 - 08:03:15 CDT)
  - Re: Colvars Harmonic Bias Force Direction Mortimer Hemmit (Wed Sep 02 2020 - 20:02:03 CDT)
Wrong number of basis-sets stored! è¾›å¿—å®� (Tue Sep 01 2020 - 21:10:17 CDT)
- Re: Wrong number of basis-sets stored! Acharya, Atanu (Wed Sep 02 2020 - 00:10:54 CDT)
  - Re:Re: Wrong number of basis-sets stored! è¾›å¿—å®� (Wed Sep 02 2020 - 09:48:38 CDT)
PME in PairInteraction Calculations Matthew Guberman-Pfeffer (Tue Sep 01 2020 - 00:01:51 CDT)
- Re: PME in PairInteraction Calculations Peter Freddolino (Tue Sep 01 2020 - 00:23:26 CDT)
  - Re: PME in PairInteraction Calculations Matthew Guberman-Pfeffer (Wed Sep 02 2020 - 01:01:25 CDT)
Problems in sharing of replicas in REMD Anup Prasad (Mon Aug 31 2020 - 18:03:59 CDT)
Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sat Aug 29 2020 - 18:36:01 CDT)
- Re: Error when using namdplot Peter Freddolino (Sat Aug 29 2020 - 22:26:08 CDT)
  - Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:18:40 CDT)
- Re: Error when using namdplot Kodituwakku,Dimuthu Nirmani (Sun Aug 30 2020 - 09:33:47 CDT)
QM atom cannot be fixed in space è¾›å¿—å®� (Sat Aug 29 2020 - 07:51:21 CDT)
- Re: QM atom cannot be fixed in space Alex Balaeff (Sat Aug 29 2020 - 09:29:48 CDT)
  - Re: Re: QM atom cannot be fixed in space Alex Balaeff (Mon Aug 31 2020 - 00:41:26 CDT)
  - Re: Re: Re: QM atom cannot be fixed in space Alex Balaeff (Tue Sep 01 2020 - 23:47:18 CDT)
Re: : Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Aug 28 2020 - 18:21:18 CDT)
- Re: Re: The HIP version of NAMD gets wrong results when computing on more than one node å¼ é©æ´² (Fri Aug 28 2020 - 23:36:12 CDT)
Problem with BEUS in NAMD 2.14 David Tang (Mon Aug 24 2020 - 14:29:10 CDT)
- Re: Problem with BEUS in NAMD 2.14 Giacomo Fiorin (Mon Aug 24 2020 - 14:42:34 CDT)
Re: namd-l digest V1 #2927 Raman Preet Singh (Mon Aug 24 2020 - 01:45:58 CDT)
Running NAMD - 2.14 - SMP - Verbs - CUDA Bassam Haddad (Wed Aug 19 2020 - 20:56:19 CDT)
- Re: Running NAMD - 2.14 - SMP - Verbs - CUDA Bassam Haddad (Thu Aug 20 2020 - 16:56:36 CDT)
  - Re: Running NAMD - 2.14 - SMP - Verbs - CUDA Victor Kwan (Sun Aug 23 2020 - 10:42:05 CDT)
Simulation Crash SMD Coarse-Grained Ethan Croitoru (Wed Aug 19 2020 - 15:24:01 CDT)
- Re: Simulation Crash SMD Coarse-Grained Victor Kwan (Sun Aug 23 2020 - 10:44:55 CDT)
JS plugin issues when constructing large systems Cavalleri A. (Mon Aug 17 2020 - 13:37:22 CDT)
Error in fftk during bond opt using VMD 1.9.3 Faisal, H M Nasrullah (Mon Aug 17 2020 - 10:08:00 CDT)
Re: namd-l digest V1 #2923 Raman Preet Singh (Mon Aug 17 2020 - 01:47:09 CDT)
- Re: Re: namd-l digest V1 #2923 Asmi Mahmood (Mon Aug 17 2020 - 02:36:33 CDT)
  - AW: Re: namd-l digest V1 #2923 Norman Geist (Mon Aug 17 2020 - 03:14:07 CDT)
- Re: Re: namd-l digest V1 #2923 Pratik Narain Srivastava (Mon Aug 17 2020 - 02:49:19 CDT)
Low simulation speed with 24 processors Asmi Mahmood (Sun Aug 16 2020 - 12:39:26 CDT)
Hi Asmi Mahmood (Sun Aug 16 2020 - 12:38:21 CDT)
Re: vmd-l: PME boolean HEMANTH H (Fri Aug 14 2020 - 03:20:48 CDT)
Resuming / Resubmitting RAMD simulations on a HPC Gerald Keller (Thu Aug 13 2020 - 02:51:37 CDT)
Annealing stepin QwikMD of VMD soodabeh ghaffari (Wed Aug 12 2020 - 17:50:01 CDT)
Re: ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 12:44:55 CDT)
- Re: ABF protocol to calculate PMF Giacomo Fiorin (Wed Aug 12 2020 - 13:20:17 CDT)
  - Re: ABF protocol to calculate PMF Giacomo Fiorin (Wed Aug 12 2020 - 13:36:21 CDT)
    - Re: ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 14:12:48 CDT)
ABF protocol to calculate PMF Rukhsar Ali (Wed Aug 12 2020 - 11:13:53 CDT)
Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 11 2020 - 19:50:48 CDT)
- Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Gumbart, JC (Sat Aug 15 2020 - 20:23:12 CDT)
  - Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 25 2020 - 15:06:12 CDT)
POSTDOCTORAL POSITION at CFM/MPC (Donostia, San Sebastian - SPAIN) Aritz Leonardo Liceranzu (Mon Aug 10 2020 - 17:04:46 CDT)
Cuboid water box issues Raman Preet Singh (Fri Aug 07 2020 - 13:29:06 CDT)
- Re: Cuboid water box issues Josh Vermaas (Fri Aug 07 2020 - 13:46:30 CDT)
- Re: Cuboid water box issues Peter Freddolino (Fri Aug 07 2020 - 15:16:50 CDT)
  - RE: Cuboid water box issues Raman Preet Singh (Tue Aug 11 2020 - 13:28:55 CDT)
Postdoctoral opening at MSU Josh Vermaas (Thu Aug 06 2020 - 09:46:56 CDT)
- Re: Postdoctoral opening at MSU Shailesh Kumar Panday (Sat Aug 08 2020 - 21:05:46 CDT)
QM/MM simulations with live solvent Oleksii Zdorevskyi (Thu Aug 06 2020 - 05:15:26 CDT)
- Re: QM/MM simulations with live solvent Marcelo C. R. Melo (Fri Aug 07 2020 - 15:34:00 CDT)
  - Re: QM/MM simulations with live solvent Oleksii Zdorevskyi (Thu Aug 20 2020 - 08:43:52 CDT)
    - Re: QM/MM simulations with live solvent Marcelo C. R. Melo (Fri Aug 21 2020 - 09:51:26 CDT)
Extra frame at start of each trajectory Ethan Croitoru (Wed Aug 05 2020 - 14:23:47 CDT)
- Re: Extra frame at start of each trajectory Josh Vermaas (Wed Aug 05 2020 - 14:33:43 CDT)
Possible issue with NAMD_2.13_Linux-x86_64-multicore-CUDA version for Drude support HEMANTH H (Wed Aug 05 2020 - 10:11:08 CDT)
- Re: Possible issue with NAMD_2.13_Linux-x86_64-multicore-CUDA version for Drude support JC Gumbart (Wed Aug 05 2020 - 15:44:38 CDT)
Alchemical Transformation for calculation of standard binding free energies Cameron Grant (Wed Aug 05 2020 - 04:44:58 CDT)
Senior Investigator/ Investigator Position (Molecular Dynamics) at Silicon Therapeutics Joao Ribeiro (Mon Aug 03 2020 - 12:51:52 CDT)
Senior Investigator/ Investigator Position (Quantum Mechanics) at Silicon Therapeutics Joao Ribeiro (Mon Aug 03 2020 - 07:50:06 CDT)
Parameters for molecular N2 Raman Preet Singh (Fri Jul 31 2020 - 13:29:47 CDT)
[3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Thu Jul 30 2020 - 18:43:15 CDT)
- Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. yjcoshc (Thu Jul 30 2020 - 20:17:40 CDT)
  - Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Fri Jul 31 2020 - 11:01:46 CDT)
    - Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. yjcoshc (Fri Jul 31 2020 - 14:43:11 CDT)
  - Re: [3.0alpha5] Low global CUDA exclusion count. System is stable without cudaSOAIntegrate or without rigidBonds. Michael Von Domaros (Mon Aug 03 2020 - 18:39:14 CDT)
CUDA Error Roshan Shrestha (Wed Jul 29 2020 - 13:22:36 CDT)
Slow performance over multi-core processor and CUDA build Roshan Shrestha (Tue Jul 28 2020 - 05:01:14 CDT)
- Re: Slow performance over multi-core processor and CUDA build Ashkan Shekaari (Tue Jul 28 2020 - 07:25:29 CDT)
NAMD on 24 threads Asmi Mahmood (Mon Jul 27 2020 - 04:06:28 CDT)
- Re: NAMD on 24 threads Ashkan Shekaari (Mon Jul 27 2020 - 07:03:54 CDT)
  - Re: NAMD on 24 threads Pratik Narain Srivastava (Mon Jul 27 2020 - 12:10:53 CDT)
error with namd2_ti.pl script Qasim Pars (Sat Jul 25 2020 - 23:42:22 CDT)
- Re: error with namd2_ti.pl script yjcoshc (Sun Jul 26 2020 - 12:58:50 CDT)
  - Re: error with namd2_ti.pl script Qasim Pars (Tue Jul 28 2020 - 15:01:12 CDT)
    - Re: error with namd2_ti.pl script Mateusz Bieniek (Wed Jul 29 2020 - 09:14:53 CDT)
NAMD CUDA specification Asmi Mahmood (Sat Jul 25 2020 - 01:33:55 CDT)
Missing frames in DCD header when continue from segment without DCD output Maximilian Ebert (Fri Jul 24 2020 - 15:30:32 CDT)
PhD Position In Computational Structural Biology Of Membrane Proteins Marawan Hussien (Thu Jul 23 2020 - 17:49:08 CDT)
FATAL ERROR: EOF ENCOUNTERED WHILE READING BONDS FROM PSF FILE Jose Correa (Thu Jul 23 2020 - 12:28:07 CDT)
- Re: FATAL ERROR: EOF ENCOUNTERED WHILE READING BONDS FROM PSF FILE Josh Vermaas (Thu Jul 23 2020 - 13:19:16 CDT)
FATAL ERROR: must have same number of LP hosts as lone pairs Selemon Bekele (Wed Jul 22 2020 - 16:33:33 CDT)
- Re: FATAL ERROR: must have same number of LP hosts as lone pairs yjcoshc (Wed Jul 22 2020 - 16:51:03 CDT)
TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG Mateusz Bieniek (Sat Jul 18 2020 - 09:30:33 CDT)
- Re: TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG Peter Freddolino (Sun Jul 19 2020 - 20:54:13 CDT)
  - Re: TI alchemical transformation of a ring atom: small partial charge difference affects strongly dG Mateusz Bieniek (Tue Jul 21 2020 - 07:33:17 CDT)
Free-energy of association of transmembrane helices Ethan Croitoru (Fri Jul 17 2020 - 20:05:40 CDT)
- Re: Free-energy of association of transmembrane helices Giacomo Fiorin (Sat Jul 18 2020 - 07:36:17 CDT)
issues with QMMM and parameters Francesco Pietra (Wed Jul 15 2020 - 02:23:43 CDT)
obtaining the viscosity of mixture from NAMD output file Kosar Khajeh (Wed Jul 15 2020 - 02:21:23 CDT)
- obtaining the viscosity of mixture from NAMD output file Kosar Khajeh (Thu Jul 16 2020 - 08:13:30 CDT)
NAMD overestimates the hydration free energy with Drude force field Qasim Pars (Tue Jul 14 2020 - 12:10:01 CDT)
Degrees of Freedom in REST2 Alex Hummels (Sun Jul 12 2020 - 13:31:49 CDT)
- Re: Degrees of Freedom in REST2 JC Gumbart (Sun Jul 12 2020 - 18:13:31 CDT)
Dcd file abnormal termination please help Kushal Roy (Sun Jul 12 2020 - 06:43:28 CDT)
- Re: Dcd file abnormal termination please help Chandni Tiwari (Sun Jul 12 2020 - 08:27:40 CDT)
  - Re: Dcd file abnormal termination please help Kushal Roy (Sun Jul 12 2020 - 12:05:21 CDT)
Restarting aborted NAMD run Raman Preet Singh (Sun Jul 12 2020 - 03:56:22 CDT)
- Re: Restarting aborted NAMD run Adupa Vasista (Sun Jul 12 2020 - 10:05:41 CDT)
- Re: Restarting aborted NAMD run Alex Balaeff (Sun Jul 12 2020 - 10:50:38 CDT)
  - RE: Restarting aborted NAMD run Raman Preet Singh (Wed Aug 12 2020 - 12:40:45 CDT)
Dynamic switching GPU/CPU minimization Maximilian Ebert (Sat Jul 11 2020 - 08:49:50 CDT)
Pair interaction calculations of the QM/MM system Alex Balaeff (Tue Jul 07 2020 - 18:44:21 CDT)
Re: scripts to generate initial boxes of solvents Josh Vermaas (Sun Jul 05 2020 - 14:51:48 CDT)
- Re: Re: scripts to generate initial boxes of solvents Francesco Pietra (Mon Jul 06 2020 - 10:01:03 CDT)
  - Re: Re: scripts to generate initial boxes of solvents Josh Vermaas (Mon Jul 06 2020 - 10:18:03 CDT)
    - Re: Re: scripts to generate initial boxes of solvents Francesco Pietra (Mon Jul 06 2020 - 10:25:06 CDT)
Equilibrated boxes of organic solvents Francesco Pietra (Sat Jul 04 2020 - 11:46:15 CDT)
- Re: Equilibrated boxes of organic solvents Josh Vermaas (Sat Jul 04 2020 - 22:57:46 CDT)
  - Re: Equilibrated boxes of organic solvents Francesco Pietra (Sun Jul 05 2020 - 09:27:40 CDT)
    - Re: Equilibrated boxes of organic solvents Joseph Farran (Sun Jul 05 2020 - 10:34:44 CDT)
    - Re: Equilibrated boxes of organic solvents Josh Vermaas (Sun Jul 05 2020 - 14:02:20 CDT)
MOPAC output file analysis M. A (Fri Jul 03 2020 - 14:53:05 CDT)
The HIP version of NAMD gets wrong results when computing on more than one node å¼ é©æ´² (Fri Jul 03 2020 - 04:58:16 CDT)
- Re: The HIP version of NAMD gets wrong results when computing on more than one node Josh Vermaas (Fri Jul 03 2020 - 05:54:33 CDT)
  - Re: The HIP version of NAMD gets wrong results when computing on more than one node å¼ é©æ´² (Fri Jul 03 2020 - 06:36:12 CDT)
Questions about soluteScalingFactor in REST2 Alex Hummels (Thu Jul 02 2020 - 17:19:11 CDT)
- Re: Questions about soluteScalingFactor in REST2 Geist, Norman (Fri Jul 03 2020 - 04:34:41 CDT)
CpHMD: Warning when building atom of unknown mass (psfgen) Aalap Parikh (Tue Jun 30 2020 - 15:35:37 CDT)
- Re: CpHMD: Warning when building atom of unknown mass (psfgen) Brian Radak (Tue Jun 30 2020 - 18:18:30 CDT)
RAMD seed number Aashish Bhatt (Mon Jun 29 2020 - 08:31:10 CDT)
- Re: RAMD seed number Josh Vermaas (Mon Jun 29 2020 - 17:26:59 CDT)
  - Re: RAMD seed number Aashish Bhatt (Tue Jun 30 2020 - 01:02:58 CDT)
  - Re: RAMD seed number Aashish Bhatt (Wed Aug 05 2020 - 05:31:11 CDT)
NAMD configuration file error Ratnika Sharma (Sun Jun 28 2020 - 15:45:27 CDT)
- Re: NAMD configuration file error HEMANTH H (Sun Jun 28 2020 - 21:06:26 CDT)
  - Re: NAMD configuration file error HEMANTH H (Mon Jun 29 2020 - 02:40:50 CDT)
Patch bond not formed Kodituwakku,Dimuthu Nirmani (Sun Jun 28 2020 - 00:58:56 CDT)
- Re: Patch bond not formed Josh Vermaas (Sun Jun 28 2020 - 16:42:45 CDT)
  - Re: Patch bond not formed Kodituwakku,Dimuthu Nirmani (Sun Jun 28 2020 - 16:46:19 CDT)
    - Re: Patch bond not formed Josh Vermaas (Sun Jun 28 2020 - 17:33:31 CDT)
How to best use GPUs Itamar Kass (Thu Jun 25 2020 - 05:06:46 CDT)
- Re: How to best use GPUs Giacomo Fiorin (Thu Jun 25 2020 - 07:51:45 CDT)
  - Re: How to best use GPUs Josh Vermaas (Thu Jun 25 2020 - 11:10:51 CDT)
    - Re: How to best use GPUs Itamar Kass (Thu Jun 25 2020 - 12:20:37 CDT)
How to restart a FEP simulation Qasim Pars (Thu Jun 25 2020 - 02:37:46 CDT)
- Re: How to restart a FEP simulation JÃ©rÃ´me HÃ©nin (Thu Jun 25 2020 - 07:12:10 CDT)
  - Re: How to restart a FEP simulation Qasim Pars (Thu Jun 25 2020 - 08:03:45 CDT)
  - Re: How to restart a FEP simulation JÃ©rÃ´me HÃ©nin (Fri Jun 26 2020 - 07:19:35 CDT)
npt simulation where only one of the dimensions is fixed Oleksii Zdorevskyi (Wed Jun 24 2020 - 01:29:50 CDT)
Protein-ligand complex Raman Preet Singh (Tue Jun 23 2020 - 08:47:56 CDT)
- Re: Protein-ligand complex Pratik Narain Srivastava (Tue Jun 23 2020 - 09:56:45 CDT)
how does NAMD know which residue to (de)couple Qasim Pars (Sun Jun 21 2020 - 17:28:19 CDT)
- Re: how does NAMD know which residue to (de)couple Michael Robinson (Sun Jun 21 2020 - 21:26:06 CDT)
  - Re: how does NAMD know which residue to (de)couple Qasim Pars (Sun Jun 21 2020 - 23:32:28 CDT)
    - Re: how does NAMD know which residue to (de)couple Chris Chipot (Mon Jun 22 2020 - 02:22:06 CDT)
Warning: DUPLICATE ANGLE/BOND/DIHEDRAL ENTRY FOR ............... Indrajit Deb (Wed Jun 17 2020 - 00:03:18 CDT)
Re: Transforming ORCA data to CHARMM format GIUSEPPE LEONARDO LICARI (Thu Jun 11 2020 - 08:58:22 CDT)
Transforming ORCA data to CHARMM format Peter Mawanga (Thu Jun 11 2020 - 06:32:40 CDT)
how to run flexible fitting for structure with helical symmetry Zhang Yan (Thu Jun 11 2020 - 03:24:31 CDT)
how to disable the periodic condition tracking two atom distance Jiali Wang (Wed Jun 10 2020 - 12:54:51 CDT)
- Re: how to disable the periodic condition tracking two atom distance Josh Vermaas (Wed Jun 10 2020 - 15:10:35 CDT)
  - Re: [External Email] Re: how to disable the periodic condition tracking two atom distance Jiali Wang (Thu Jun 11 2020 - 11:49:54 CDT)
ERROR: Atoms (still) moving too fast Justine Raymond (Wed Jun 10 2020 - 09:23:34 CDT)
CPU/GPU Distribution Youssef Elmougy (Tue Jun 09 2020 - 16:44:59 CDT)
(no subject) shyam sharma (Mon Jun 08 2020 - 04:29:00 CDT)
How can I analyse QMMM log file? M. A (Sun Jun 07 2020 - 02:43:55 CDT)
Psfgen, Disulfide Linkages, and the Drude Polarizable Force Field Michael Robinson (Fri Jun 05 2020 - 03:31:05 CDT)
Re: Error during simulation shyam sharma (Thu Jun 04 2020 - 22:54:10 CDT)
Bond between custom ligand and protein sidechain McGuire, Kelly (Thu Jun 04 2020 - 20:05:51 CDT)
Non-SLI GPUs in NAMD Raman Preet Singh (Thu Jun 04 2020 - 12:56:58 CDT)
- Re: Non-SLI GPUs in NAMD Josh Vermaas (Thu Jun 04 2020 - 14:59:36 CDT)
Comparison of electric field between MD simulation and Experiments Mani Kandan (Sun May 31 2020 - 11:47:55 CDT)
Question about QMMM simulation M. A (Sun May 31 2020 - 06:31:38 CDT)
- Re: Question about QMMM simulation Giacomo Fiorin (Sun May 31 2020 - 11:02:50 CDT)
  - Re: Question about QMMM simulation M. A (Sun May 31 2020 - 15:03:04 CDT)
Drude polarizable force field NicolÃ¡s Marcelo Rozas Castro (Sun May 31 2020 - 04:13:43 CDT)
- Re: Drude polarizable force field Victor Kwan (Sun May 31 2020 - 09:22:27 CDT)
Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Sebastian S (Sun May 31 2020 - 00:20:07 CDT)
- Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Aksimentiev, Aleksei (Sun May 31 2020 - 09:27:31 CDT)
  - Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Sebastian S (Sun May 31 2020 - 11:58:40 CDT)
    - Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Aksimentiev, Aleksei (Sun May 31 2020 - 14:51:36 CDT)
    - Re: Files from "Hands-on" Workshop on Structural DNA Nanotechnology at Urbana Sebastian S (Sun May 31 2020 - 15:13:33 CDT)
System Drifts Along Z-Axis Bassam Haddad (Fri May 29 2020 - 14:36:49 CDT)
- Re: System Drifts Along Z-Axis Peter Freddolino (Sun May 31 2020 - 13:35:00 CDT)
  - Re: System Drifts Along Z-Axis Bassam Haddad (Sun May 31 2020 - 14:09:37 CDT)
  - Re: System Drifts Along Z-Axis Bassam Haddad (Sun May 31 2020 - 16:16:52 CDT)
    - Re: System Drifts Along Z-Axis Giacomo Fiorin (Sun May 31 2020 - 16:25:07 CDT)
    - Re: System Drifts Along Z-Axis Bassam Haddad (Sun May 31 2020 - 16:56:05 CDT)
error: minimizer slowly moving xxx atoms with bad contacts downhill Ceren Ciraci (Tue May 26 2020 - 10:45:45 CDT)
- Re: error: minimizer slowly moving xxx atoms with bad contacts downhill Giacomo Fiorin (Tue May 26 2020 - 10:50:43 CDT)
  - Re: error: minimizer slowly moving xxx atoms with bad contacts downhill Ceren Ciraci (Tue May 26 2020 - 13:33:09 CDT)
    - Re: error: minimizer slowly moving xxx atoms with bad contacts downhill Giacomo Fiorin (Tue May 26 2020 - 15:16:08 CDT)
Specifying a pull direction with COLVARS Selemon Bekele (Mon May 25 2020 - 23:52:47 CDT)
- Re: Specifying a pull direction with COLVARS JÃ©rÃ´me HÃ©nin (Tue May 26 2020 - 09:19:04 CDT)
Setting up / Running NAMD on HPC Gerald Keller (Mon May 25 2020 - 03:56:34 CDT)
- Re: Setting up / Running NAMD on HPC Renfro, Michael (Mon May 25 2020 - 09:23:50 CDT)
  - Re: Re: Setting up / Running NAMD on HPC Gerald Keller (Mon May 25 2020 - 14:17:40 CDT)
    - Re: Re: Setting up / Running NAMD on HPC Josh Vermaas (Mon May 25 2020 - 16:44:10 CDT)
    - Re: Re: Setting up / Running NAMD on HPC Victor Kwan (Mon May 25 2020 - 16:54:55 CDT)
Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Mon May 25 2020 - 00:35:20 CDT)
- Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Josh Vermaas (Mon May 25 2020 - 17:35:40 CDT)
  - Re: Is there a way to stop a MD run before the END_OF_RUN timestep? Cardenas, Alfredo E (Tue May 26 2020 - 14:44:22 CDT)
Negative Forces in SMD Simulations Souvik Dey (Fri May 22 2020 - 16:40:25 CDT)
- Re: Negative Forces in SMD Simulations Gumbart, JC (Tue May 26 2020 - 13:17:03 CDT)
  - Re: Negative Forces in SMD Simulations Souvik Dey (Tue May 26 2020 - 13:21:19 CDT)
Dcdfreq Variable Value Question Oscar Bastidas (Fri May 22 2020 - 15:23:45 CDT)
- Re: Dcdfreq Variable Value Question Mortimer Hemmit (Fri May 22 2020 - 17:28:59 CDT)
NAMD 3.0 alpha, operating system requirements Nicholas M. Glykos (Fri May 22 2020 - 13:19:02 CDT)
solvation with SWM4 water model Qasim Pars (Thu May 21 2020 - 19:37:21 CDT)
- Re: solvation with SWM4 water model HEMANTH H (Fri May 22 2020 - 09:26:15 CDT)
  - Re: solvation with SWM4 water model Giacomo Fiorin (Fri May 22 2020 - 09:47:43 CDT)
Negative Forces in SMD Simulations Souvik Dey (Thu May 21 2020 - 16:45:28 CDT)
- Re: Negative Forces in SMD Simulations Josh Vermaas (Thu May 21 2020 - 18:16:52 CDT)
Format of 'dcdfreq' field in conf file Oscar Bastidas (Thu May 21 2020 - 01:09:00 CDT)
- Re: Format of 'dcdfreq' field in conf file Axel Kohlmeyer (Thu May 21 2020 - 01:19:26 CDT)
  - Re: Format of 'dcdfreq' field in conf file Oscar Bastidas (Thu May 21 2020 - 01:19:05 CDT)
Fwd: Inquiry regarding benchmark simulations David Hardy (Wed May 20 2020 - 17:15:38 CDT)
- Re: Fwd: Inquiry regarding benchmark simulations John Stone (Sat May 23 2020 - 02:15:28 CDT)
Issue in reading the soluteScalingFile for REST2 GILLET Natacha (Sat May 16 2020 - 01:56:52 CDT)
how to set the input file for the free energy calculations with CHARMM Drude force field Qasim Pars (Fri May 15 2020 - 17:36:33 CDT)
Re: FATAL ERROR: Charge placement error in QM-MM bond. M. A (Mon May 11 2020 - 15:01:49 CDT)
- Fwd: FATAL ERROR: Charge placement error in QM-MM bond. M. A (Thu May 14 2020 - 05:39:54 CDT)
Replica exchange on GPU with OPA network and Slurm Thibaut Very (Mon May 11 2020 - 03:20:50 CDT)
- Re: Replica exchange on GPU with OPA network and Slurm Geist, Norman (Mon May 11 2020 - 05:24:54 CDT)
FATAL ERROR: Charge placement error in QM-MM bond. M. A (Mon May 11 2020 - 01:43:20 CDT)
Re: Using NAMD and Orca together -- a QM/MM job David Baker (Thu May 07 2020 - 10:19:43 CDT)
Using NAMD and Orca together -- a QM/MM job David Baker (Thu May 07 2020 - 06:12:57 CDT)
Bypassing MM parameterization of ligand in QMMM Francesco Pietra (Wed May 06 2020 - 02:49:55 CDT)
- Fwd: Bypassing MM parameterization of ligand in QMMM Francesco Pietra (Wed May 06 2020 - 03:10:29 CDT)
Langevin dynamics and random seeds Morgan Packer (Tue May 05 2020 - 17:30:54 CDT)
- Re: Langevin dynamics and random seeds Peter Freddolino (Tue May 05 2020 - 19:20:39 CDT)
NAMD job takes long time to finish 1 ns equilibration Khoualdi Asma Feriel (Tue May 05 2020 - 14:57:27 CDT)
- Re: NAMD job takes long time to finish 1 ns equilibration Giacomo Fiorin (Tue May 05 2020 - 17:46:54 CDT)
Re: Rattle algorithm error: when to minimise Khoualdi Asma Feriel (Tue May 05 2020 - 14:49:42 CDT)
Parametrization of zinc ion (+2) in using CHARMM force field. varun dewaker (Tue May 05 2020 - 00:26:12 CDT)
pbc correction for nve unwrap trajectory aiming calculation of diffusion coefficient Santanu Santra (Mon May 04 2020 - 23:54:19 CDT)
actual production MD L- (Mon May 04 2020 - 20:01:10 CDT)
- Re: actual production MD L- (Tue May 05 2020 - 07:41:43 CDT)
  - Re: actual production MD Oscar Bastidas (Tue May 05 2020 - 14:44:50 CDT)
Box of Water L- (Mon May 04 2020 - 19:12:03 CDT)
- Re: Box of Water HEMANTH H (Mon May 04 2020 - 21:53:07 CDT)
  - Re: Box of Water Oscar Bastidas (Tue May 05 2020 - 14:51:44 CDT)
    - Re: Box of Water Josh Vermaas (Tue May 05 2020 - 18:09:35 CDT)
DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 05:08:10 CDT)
- Re: DCD File Not Generating Aashish Bhatt (Sat May 02 2020 - 05:21:53 CDT)
- Re: DCD File Not Generating Ashkan Shekaari (Sat May 02 2020 - 05:30:42 CDT)
  - Re: DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 05:31:03 CDT)
    - Re: DCD File Not Generating Michael Robinson (Sat May 02 2020 - 08:14:51 CDT)
    - Re: DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 15:35:17 CDT)
- Re: DCD File Not Generating Josh Vermaas (Sat May 02 2020 - 10:12:44 CDT)
  - Re: DCD File Not Generating Oscar Bastidas (Sat May 02 2020 - 15:50:36 CDT)
When to use a semicolon in a *.conf file? Oscar Bastidas (Wed Apr 29 2020 - 23:14:07 CDT)
- Re: When to use a semicolon in a *.conf file? Josh Vermaas (Thu Apr 30 2020 - 07:50:12 CDT)
  - Re: When to use a semicolon in a *.conf file? Oscar Bastidas (Thu Apr 30 2020 - 22:28:25 CDT)
Run NAMD without GPU L- (Sun Apr 26 2020 - 06:33:50 CDT)
- Re: Run NAMD without GPU Josh Vermaas (Sun Apr 26 2020 - 07:29:45 CDT)
qmmm simulation and question for md analysis M. A (Mon Apr 20 2020 - 03:59:45 CDT)
- Re: qmmm simulation and question for md analysis Francesco Pietra (Mon Apr 20 2020 - 05:16:02 CDT)
  - Re: qmmm simulation and question for md analysis M. A (Sat May 09 2020 - 01:55:18 CDT)
Patch grid too small error in first production run Khoualdi Asma Feriel (Sun Apr 19 2020 - 14:29:06 CDT)
- Re: Patch grid too small error in first production run Josh Vermaas (Sun Apr 19 2020 - 16:51:22 CDT)
  - Re: Patch grid too small error in first production run Josh Vermaas (Sun Apr 19 2020 - 20:19:53 CDT)
    - Re: Patch grid too small error in first production run Khoualdi Asma Feriel (Thu Apr 30 2020 - 12:16:01 CDT)
- Re: Patch grid too small error in first production run Ashkan Shekaari (Sun Apr 19 2020 - 18:10:32 CDT)
Receptor-ligand binding energy from QMMM Francesco Pietra (Sat Apr 18 2020 - 03:52:40 CDT)
Re: FATAL ERROR: Error running command for QM forces calculation. M. A (Fri Apr 17 2020 - 11:53:08 CDT)
- Re: FATAL ERROR: Error running command for QM forces calculation. M. A (Fri Apr 17 2020 - 12:06:08 CDT)
Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:42:25 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 11:52:28 CDT)
  - Fwd: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 11:55:50 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 12:29:46 CDT)
- Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Tue Apr 28 2020 - 12:06:01 CDT)
  - Re: Error: Number of NGauss expected in AddNewGTOs Pawel Kedzierski (Tue Apr 28 2020 - 15:10:01 CDT)
    - Re: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Wed Apr 29 2020 - 01:59:05 CDT)
Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:09:36 CDT)
- Fwd: Error: Number of NGauss expected in AddNewGTOs Francesco Pietra (Thu Apr 16 2020 - 10:17:09 CDT)
Issue about replica-exchangeumbrella sampling by 16 threads è¾›å¿—å®� (Thu Apr 16 2020 - 04:12:37 CDT)
- Re: Issue about replica-exchangeumbrella sampling by 16 threads Josh Vermaas (Thu Apr 16 2020 - 11:33:00 CDT)
  - Fw: Re: Issue about replica-exchangeumbrella sampling by 16 threads è¾›å¿—å®� (Thu Apr 16 2020 - 19:40:50 CDT)
Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... zeynab hosseini (Wed Apr 15 2020 - 00:07:27 CDT)
- Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... Giacomo Fiorin (Thu Apr 16 2020 - 09:13:14 CDT)
  - Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... Giacomo Fiorin (Thu Apr 16 2020 - 13:05:59 CDT)
    - Re: Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... zeynab hosseini (Tue Sep 01 2020 - 12:52:30 CDT)
Issues with vdW for non existing atom Francesco Pietra (Wed Apr 15 2020 - 10:29:14 CDT)
- Re: Issues with vdW for non existing atom Pratik Narain Srivastava (Wed Apr 15 2020 - 10:48:04 CDT)
  - Re: Issues with vdW for non existing atom Francesco Pietra (Wed Apr 15 2020 - 15:55:35 CDT)
(no subject) ROPÃ“N-PALACIOS G. (Tue Apr 14 2020 - 21:25:41 CDT)
minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 09:37:29 CDT)
- Re: minimise in restarting first equilibration step Josh Vermaas (Mon Apr 13 2020 - 12:16:35 CDT)
  - Re: minimise in restarting first equilibration step Khoualdi Asma Feriel (Mon Apr 13 2020 - 12:24:18 CDT)
Compile NAMD on Windows 64 bit; nocuda, multicore Mortimer Hemmit (Sun Apr 12 2020 - 17:36:46 CDT)
- Re: Compile NAMD on Windows 64 bit; nocuda, multicore Mortimer Hemmit (Mon Nov 30 2020 - 14:39:09 CST)
QwikMD Error: child killed: unknown signal Frank Lam (Sun Apr 12 2020 - 13:29:06 CDT)
- Re: QwikMD Error: child killed: unknown signal Joao Ribeiro KS (Mon Apr 13 2020 - 09:25:39 CDT)
rmsd colvars atom definition Francesco Pietra (Fri Apr 10 2020 - 01:44:55 CDT)
- Re: rmsd colvars atom definition JÃ©rÃ´me HÃ©nin (Fri Apr 10 2020 - 03:05:35 CDT)
  - Re: rmsd colvars atom definition Francesco Pietra (Fri Apr 10 2020 - 05:33:54 CDT)
.coor and .vel output files not generated Khoualdi Asma Feriel (Thu Apr 09 2020 - 21:32:20 CDT)
- Re: .coor and .vel output files not generated Josh Vermaas (Thu Apr 09 2020 - 21:46:58 CDT)
  - Re: .coor and .vel output files not generated Khoualdi Asma Feriel (Fri Apr 10 2020 - 00:35:08 CDT)
  - Re: .coor and .vel output files not generated Khoualdi Asma Feriel (Fri Apr 10 2020 - 11:12:24 CDT)
- Re: .coor and .vel output files not generated JC Gumbart (Thu Apr 09 2020 - 23:05:41 CDT)
Forces in QM/MM calculations nikolaev_at_spbau.ru (Wed Apr 08 2020 - 12:57:07 CDT)
FATAL ERROR: Error running command for QM forces calculation. M. A (Tue Apr 07 2020 - 10:31:12 CDT)
PSF for Cyclic-Branched Peptides Hendrik SchrÃ¶der (Sun Apr 05 2020 - 17:20:18 CDT)
- Re: PSF for Cyclic-Branched Peptides Aravinda Munasinghe (Sun Apr 05 2020 - 19:46:40 CDT)
Error generating files with QwikMD Marcos Verissimo Alves (Sun Apr 05 2020 - 00:33:57 CDT)
- Re: Error generating files with QwikMD Joao Ribeiro KS (Thu Apr 09 2020 - 09:20:48 CDT)
Fwd: fatal error: error in qm-mm bond assignment mariano spivak (Sat Apr 04 2020 - 11:40:19 CDT)
difference between numsteps and run in step4_equilibration.inp soodabeh ghaffari (Thu Apr 02 2020 - 14:39:05 CDT)
- Re: difference between numsteps and run in step4_equilibration.inp Giacomo Fiorin (Thu Apr 02 2020 - 15:56:37 CDT)
  - Re: difference between numsteps and run in step4_equilibration.inp soodabeh ghaffari (Thu Apr 02 2020 - 15:57:49 CDT)
- Re: difference between numsteps and run in step4_equilibration.inp Josh Vermaas (Thu Apr 02 2020 - 16:00:34 CDT)
  - Re: difference between numsteps and run in step4_equilibration.inp Mortimer Hemmit (Thu Apr 02 2020 - 18:50:12 CDT)
converting gromacs topology file to namd Hadi Rahmaninejad (Wed Apr 01 2020 - 17:11:40 CDT)
- Re: converting gromacs topology file to namd Josh Vermaas (Wed Apr 01 2020 - 18:21:55 CDT)
how i can utilize 4 GPU in simulation with poor performance L- (Wed Apr 01 2020 - 11:30:13 CDT)
- Re: how i can utilize 4 GPU in simulation with poor performance Giacomo Fiorin (Wed Apr 01 2020 - 13:11:37 CDT)
- Re: [External] how i can utilize 4 GPU in simulation with poor performance Sharp, Kim (Wed Apr 01 2020 - 14:00:15 CDT)
MDFF chirality restrain error - measure imprp: empty atom index Indrajit Deb (Wed Apr 01 2020 - 11:15:57 CDT)
QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 05:49:53 CDT)
- Re: QMMM param issue Marcelo C. R. Melo (Wed Apr 01 2020 - 09:57:44 CDT)
  - Re: QMMM param issue Francesco Pietra (Wed Apr 01 2020 - 11:09:29 CDT)
using an Amber topology with OPC water model in NAMD Vlad Cojocaru (Tue Mar 31 2020 - 13:38:42 CDT)
- Re: using an Amber topology with OPC water model in NAMD Victor Kwan (Tue Mar 31 2020 - 15:34:57 CDT)
  - Re: using an Amber topology with OPC water model in NAMD Vlad Cojocaru (Tue Mar 31 2020 - 18:20:00 CDT)
Collaboration offer Raman Preet Singh (Mon Mar 30 2020 - 08:01:54 CDT)
Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 04:42:43 CDT)
- Re: Running on GPU multiple nodes Renfro, Michael (Sun Mar 29 2020 - 08:15:16 CDT)
  - Re: Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 14:22:05 CDT)
    - Re: Running on GPU multiple nodes Josh Vermaas (Sun Mar 29 2020 - 17:47:49 CDT)
    - Re: Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 21:34:14 CDT)
Unpredictably Crashes upon Restarting Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 16:56:43 CDT)
- Re: Unpredictably Crashes upon Restarting Victor Kwan (Fri Mar 27 2020 - 17:32:01 CDT)
  - Re: Unpredictably Crashes upon Restarting Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 18:00:32 CDT)
Lipids generated by VMD could not use "coordpdb" to read jiali wang (Thu Mar 26 2020 - 23:42:27 CDT)
How to avoid producing a huge DCD file? è¾›å¿—å®� (Mon Mar 23 2020 - 22:15:53 CDT)
- Re: How to avoid producing a huge DCD file? HEMANTH H (Mon Mar 23 2020 - 23:19:19 CDT)
- Re: How to avoid producing a huge DCD file? Julio Maia (Tue Mar 24 2020 - 00:09:00 CDT)
- Fw: How to avoid producing a huge DCD file? è¾›å¿—å®� (Tue Mar 24 2020 - 02:35:00 CDT)
How to fix mutex error Matthew Guberman-Pfeffer (Sat Mar 21 2020 - 22:51:27 CDT)
- Re: How to fix mutex error Victor Kwan (Sun Mar 22 2020 - 20:01:15 CDT)
  - Re: How to fix mutex error Matthew Guberman-Pfeffer (Fri Mar 27 2020 - 16:36:38 CDT)
    - Re: How to fix mutex error Victor Kwan (Fri Mar 27 2020 - 17:28:56 CDT)
acetylene Mikhail Suyetin (Wed Mar 18 2020 - 06:56:47 CDT)
- Re: acetylene Josh Vermaas (Wed Mar 18 2020 - 09:47:07 CDT)
NGRP NST2 Selemon Bekele (Tue Mar 17 2020 - 12:13:20 CDT)
- RE: NGRP NST2 Lennart Nilsson (Tue Mar 17 2020 - 12:46:38 CDT)
  - Re: NGRP NST2 Selemon Bekele (Tue Mar 17 2020 - 14:51:04 CDT)
Technical specifications for the V100 and GTX gpu cards Souvik Sinha (Tue Mar 17 2020 - 03:26:28 CDT)
- Re: Technical specifications for the V100 and GTX gpu cards Axel Kohlmeyer (Tue Mar 17 2020 - 06:32:59 CDT)
  - Re: Technical specifications for the V100 and GTX gpu cards Souvik Sinha (Fri Mar 20 2020 - 01:18:32 CDT)
Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 12:10:53 CDT)
- Re: vmd-l: Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 13:01:44 CDT)
- Re: Pair interaction calculation is not supported in CUDA version Josh Vermaas (Sun Mar 15 2020 - 14:58:45 CDT)
  - Re: Pair interaction calculation is not supported in CUDA version Adupa Vasista (Sun Mar 15 2020 - 23:48:52 CDT)
NAMD error : alloc_mempool_block: posix_memalign failed Himanshu Joshi (Fri Mar 13 2020 - 15:51:51 CDT)
Does NAMD have unit tests or how can I confirm the correctness of the simulation results of NAMD? å¼ é©æ´² (Tue Mar 10 2020 - 20:29:34 CDT)
Stability issues with POPC membrane using Drude force field Batuhan Kav (Tue Mar 10 2020 - 05:08:14 CDT)
Error Restarting Simulation Matthew Guberman-Pfeffer (Mon Mar 09 2020 - 12:46:34 CDT)
- Re: Error Restarting Simulation Oscar Bastidas (Mon Mar 09 2020 - 15:00:52 CDT)
Different Velocity or Margin Errors for Restarted Simulation Matthew Guberman-Pfeffer (Mon Mar 09 2020 - 09:08:14 CDT)
NAMD performance Stefano Guglielmo (Thu Mar 05 2020 - 09:05:31 CST)
- Re: NAMD performance Victor Kwan (Thu Mar 05 2020 - 11:18:09 CST)
  - Re: NAMD performance Josh Vermaas (Thu Mar 05 2020 - 15:03:07 CST)
MD with 3-site CO model Nadia Elghobashi-Meinhardt (Wed Mar 04 2020 - 08:24:51 CST)
adding peptide constraint in NAMD configuration file soodabeh ghaffari (Tue Mar 03 2020 - 22:49:20 CST)
- Re: adding peptide constraint in NAMD configuration file Giacomo Fiorin (Wed Mar 04 2020 - 08:03:49 CST)
  - Re: adding peptide constraint in NAMD configuration file soodabeh ghaffari (Wed Mar 04 2020 - 08:44:22 CST)
    - Re: adding peptide constraint in NAMD configuration file Giacomo Fiorin (Wed Mar 04 2020 - 08:55:20 CST)
    - Re: adding peptide constraint in NAMD configuration file Josh Vermaas (Wed Mar 04 2020 - 09:22:20 CST)
question to run namd2 with multiple CPUs Yu, Tao (Fri Feb 28 2020 - 16:10:20 CST)
- Re: question to run namd2 with multiple CPUs Josh Vermaas (Fri Feb 28 2020 - 16:29:09 CST)
  - Re: question to run namd2 with multiple CPUs Yu, Tao (Mon Mar 02 2020 - 15:08:04 CST)
- Re: question to run namd2 with multiple CPUs Victor Kwan (Thu Mar 05 2020 - 18:33:23 CST)
bad angle error!! ROPÃ“N-PALACIOS G. (Thu Feb 27 2020 - 21:10:45 CST)
- Re: bad angle error!! Josh Vermaas (Fri Feb 28 2020 - 07:53:17 CST)
  - Re: bad angle error!! ROPÃ“N-PALACIOS G. (Fri Feb 28 2020 - 14:51:44 CST)
Re: Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 14:28:19 CST)
- Re: Issue with preparing QM-MM Victor Kwan (Thu Feb 27 2020 - 14:41:17 CST)
  - Re: Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 16:02:54 CST)
    - Re: Issue with preparing QM-MM Victor Kwan (Thu Feb 27 2020 - 16:26:39 CST)
Issue with preparing QM-MM Francesco Pietra (Thu Feb 27 2020 - 12:32:58 CST)
QM/MM error in the charges Aashish Bhatt (Thu Feb 27 2020 - 04:14:45 CST)
- Re: QM/MM error in the charges Josh Vermaas (Thu Feb 27 2020 - 09:00:50 CST)
  - Re: QM/MM error in the charges Aashish Bhatt (Fri Feb 28 2020 - 06:44:06 CST)
AW: vmd-l: How to increase the number of core Norman Geist (Wed Feb 26 2020 - 01:59:33 CST)
- Re: AW: vmd-l: How to increase the number of core ROPÃ“N-PALACIOS G. (Wed Feb 26 2020 - 09:46:54 CST)
Swarms of Trajectrories MPI NAMD Run Ebru Ã‡etin (Tue Feb 25 2020 - 10:15:37 CST)
Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Tue Feb 25 2020 - 04:23:19 CST)
- Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sun Mar 08 2020 - 04:30:03 CDT)
  - Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sun Mar 08 2020 - 05:09:07 CDT)
- Re: FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sat Mar 14 2020 - 17:17:37 CDT)
The best initial structure of Protein-Protein complex Alireza Mansouri (Mon Feb 24 2020 - 03:54:21 CST)
- Re: The best initial structure of Protein-Protein complex ROPÃ“N-PALACIOS G. (Mon Feb 24 2020 - 09:54:28 CST)
Protocol share Ribosome ROPÃ“N-PALACIOS G. (Fri Feb 21 2020 - 09:05:33 CST)
Can NAMD 2.13 be build on Charm++ with UCX backend? å¼ é©æ´² (Fri Feb 21 2020 - 03:55:25 CST)
- Re: Can NAMD 2.13 be build on Charm++ with UCX backend? Giacomo Fiorin (Fri Feb 21 2020 - 06:30:26 CST)
  - Re: Re: Can NAMD 2.13 be build on Charm++ with UCX backend? å¼ é©æ´² (Sat Feb 22 2020 - 03:15:26 CST)
Bad global bond count! Francesco Pietra (Tue Feb 18 2020 - 15:07:46 CST)
(no subject) Francesco Pietra (Tue Feb 18 2020 - 15:05:34 CST)
- Re: Josh Vermaas (Tue Feb 18 2020 - 15:37:22 CST)
  - Re: Abhijit Gogoi (Wed Feb 19 2020 - 02:25:32 CST)
  - Re: Francesco Pietra (Wed Feb 19 2020 - 01:36:55 CST)
FATAL ERROR: Error in QM-MM bond assignment (NAMD-ORCA) M. A (Sat Feb 15 2020 - 23:45:11 CST)
Conformation Sampling tutorial: factor of 2 in monitor.sh Alexander Adams (Tue Feb 11 2020 - 13:24:21 CST)
Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 14:34:38 CST)
- Re: Hydrogen bond energy for TIP3 water Victor Kwan (Wed Feb 05 2020 - 15:58:15 CST)
  - Re: Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 16:49:02 CST)
    - Re: Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 18:25:20 CST)
  - Re: [External] Re: Hydrogen bond energy for TIP3 water Sharp, Kim (Wed Feb 05 2020 - 17:45:57 CST)
    - Re: [External] Re: Hydrogen bond energy for TIP3 water Randy J. Zauhar (Wed Feb 05 2020 - 19:13:41 CST)
Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 05 2020 - 12:12:29 CST)
- Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Wed Feb 05 2020 - 12:51:05 CST)
  - Re: Flat-bottom harmonic position restraints using colvars Daipayan Sarkar (Wed Feb 05 2020 - 13:34:38 CST)
  - Re: Flat-bottom harmonic position restraints using colvars Giacomo Fiorin (Mon Feb 10 2020 - 06:14:11 CST)
mail about cuda exculssion count Vidhya Sankar (Wed Feb 05 2020 - 06:28:37 CST)
Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Mon Feb 03 2020 - 09:50:27 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Mon Feb 03 2020 - 10:07:57 CST)
  - Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Mon Feb 03 2020 - 22:43:31 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Tue Feb 04 2020 - 09:02:41 CST)
  - Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Wed Feb 05 2020 - 08:10:34 CST)
    - Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Wed Feb 05 2020 - 09:18:50 CST)
    - Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Thu Feb 06 2020 - 00:28:01 CST)
- Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Thu Feb 06 2020 - 09:50:39 CST)
  - Re: Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Joao Ribeiro (Thu Feb 06 2020 - 10:42:41 CST)
FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Sun Feb 02 2020 - 22:00:48 CST)
- Re: FATAL ERROR in protein minimization by drude model : UNABLE TO FIND ANGLE PARAMETERS FOR CD2O1A OD2C1A LPDO1 Santanu Santra (Sun Feb 02 2020 - 22:04:18 CST)
Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 08:32:52 CST)
- Re: Cations spontaneous binding pathway with PMF calculation? Giacomo Fiorin (Fri Jan 31 2020 - 09:22:02 CST)
  - Re: [External Email] Re: Cations spontaneous binding pathway with PMF calculation? Jiali Wang (Fri Jan 31 2020 - 10:14:59 CST)
problem with TIP4P on nightly version Laura Lopes (Fri Jan 31 2020 - 04:22:42 CST)
- Re: problem with TIP4P on nightly version Laura Lopes (Fri Jan 31 2020 - 08:11:25 CST)
  - Re: Re: problem with TIP4P on nightly version Peter Freddolino (Fri Jan 31 2020 - 09:49:56 CST)
    - Re: Re: problem with TIP4P on nightly version Brian Radak (Sun Feb 02 2020 - 14:31:58 CST)
  - Re: Re: problem with TIP4P on nightly version Monika Madhavi (Tue Feb 04 2020 - 22:08:33 CST)
Solvent Heating with Rigid Bonds ben estimated.com (Sun Jan 26 2020 - 22:07:34 CST)
Why very large force reported at the starting point of constant velocity SMD run in NAMD log file? Shadi Rahnama (Sat Jan 25 2020 - 14:56:57 CST)
Topology and parameter files for flavonoid compounds Shruthi M (116011752017) Res/Bio-Tech (Fri Jan 24 2020 - 00:42:52 CST)
- Re: Topology and parameter files for flavonoid compounds Giacomo Fiorin (Fri Jan 24 2020 - 06:08:20 CST)
Re: vmd-l: NAMD and VMD Armv8-A Giacomo Fiorin (Thu Jan 23 2020 - 09:37:59 CST)
GaMD with nucleotides Francesco Pietra (Thu Jan 23 2020 - 09:30:57 CST)
- Re: GaMD with nucleotides Miao, Yinglong (Thu Jan 23 2020 - 13:42:09 CST)
Analysis of force applied to a certain atom nikolaev_at_spbau.ru (Thu Jan 23 2020 - 09:12:27 CST)
- Re: Analysis of force applied to a certain atom Giacomo Fiorin (Thu Jan 23 2020 - 09:17:59 CST)
  - Re: Analysis of force applied to a certain atom JÃ©rÃ´me HÃ©nin (Fri Jan 24 2020 - 08:44:43 CST)
    - Re: Analysis of force applied to a certain atom Giacomo Fiorin (Fri Jan 24 2020 - 08:58:42 CST)
Amber14 in NAMD 2.13 nikolaev_at_spbau.ru (Thu Jan 23 2020 - 08:57:23 CST)
- Re: Amber14 in NAMD 2.13 Brian Radak (Sat Jan 25 2020 - 10:00:20 CST)
spontaneous binding pathway with PMF calculation? Jiali Wang (Mon Jan 20 2020 - 21:42:47 CST)
GaMD config file Francesco Pietra (Mon Jan 20 2020 - 15:43:10 CST)
- Fwd: GaMD config file Francesco Pietra (Tue Jan 21 2020 - 03:26:23 CST)
Workshop on Free Energy calculations in Muenster March 11-13 2020 Vlad Cojocaru (Fri Jan 17 2020 - 03:33:13 CST)
modelling an aqueous solution of protein+hydrogen peroxide Artur Hermano (Wed Jan 15 2020 - 17:50:41 CST)
- Re: modelling an aqueous solution of protein+hydrogen peroxide Lucas Neumann (Wed Jan 15 2020 - 18:27:29 CST)
log file Alexei Rossokhin (Tue Jan 14 2020 - 08:36:53 CST)
- Re: log file Giacomo Fiorin (Tue Jan 14 2020 - 08:54:10 CST)
  - Re: log file Alexei Rossokhin (Tue Jan 14 2020 - 10:10:19 CST)
harmonic-restraints/colvars Francesco Pietra (Tue Jan 14 2020 - 03:44:06 CST)
- Re: harmonic-restraints/colvars JÃ©rÃ´me HÃ©nin (Tue Jan 14 2020 - 04:25:06 CST)
  - Re: harmonic-restraints/colvars Francesco Pietra (Tue Jan 14 2020 - 09:42:43 CST)
How to protonate GLU Kaique Gracia De SÃ¡ Billotta (Fri Jan 10 2020 - 11:56:05 CST)
Unable to calculate SMD for amber topology Aashish Bhatt (Fri Jan 10 2020 - 08:33:10 CST)
Measuring Kinetic Energy of Solvent ben estimated.com (Tue Jan 07 2020 - 17:00:00 CST)
Order of Minimizing/Heating/Equilibrating ben estimated.com (Tue Jan 07 2020 - 16:33:51 CST)
LIE protocol in QM/MM Shahar Keinan (Fri Jan 03 2020 - 07:25:04 CST)
- Re: LIE protocol in QM/MM Marcelo C. R. Melo (Fri Jan 03 2020 - 11:26:04 CST)

Last message date: Thu Dec 30 2021 - 09:20:14 CST
Archived on: Fri Dec 31 2021 - 23:17:12 CST

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