From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Wed Sep 02 2020 - 09:48:38 CDT
Dear Atanu,
Think you very much for your kindly suggestion.
I checked qmBaseDir using an namd QM/MM example (namd-QM-MM-Example) when I changed " QMSimsPerNode 10 " as " QMSimsPerNode 1', It works fine in the Dir "/dev/shm/NAMD_Example1",
However, a new errors occured again for my enzyme simulation,
[xzhfood_at_bogon YZZ-QM-MM]$ namd2 YZZ-config.ORCA-1.namd | tee YZZ-config.ORCA-1.namd.log
Charm++> No provisioning arguments specified. Running with a single PE.
Use +auto-provision to fully subscribe resources or +p1 to silence this message.
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads (PEs)
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.10.0-rc2-9-g717093c-namd-charm-6.10.0-build-2019-Oct-31-14158
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 hosts (2 sockets x 28 cores x 2 PUs = 112-way SMP)
Charm++> cpu topology info is gathered in 0.008 seconds.
Info: NAMD Git-2019-12-13 for Linux-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 61000 for multicore-linux-x86_64-iccstatic
Info: Built Fri Dec 13 02:06:04 CST 2019 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD Git-2019-12-13 Linux-x86_64-multicore 1 bogon xzhfood
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0148728 s
CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification)
Info: 64.1562 MB of memory in use based on /proc/self/stat
Info: Configuration file is YZZ-config.ORCA-1.namd
Info: Working in the current directory /home/xzhfood/mdsim/YZZ-namd/YZZ-QM-MM
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: Continuing
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
There is no .TmpOut file in my workdir, I don't know why the same parameters for the namd example works, and don't works for my enzyme , why switch to the current Dir " Working in the current directory /home/xzhfood/mdsim/YZZ-namd/YZZ-QM-MM"not "/dev/shm/NAMD_Example1", I also build a new Dir as "/dev/shm/YZZ-namd", and chmod +x "/dev/shm/YZZ-namd" make sure it is writable, but the error is the same.
Thank you for your help again.
Zhihong Xin
发件人："Acharya, Atanu" <aacharya42_at_gatech.edu>
发送日期：2020-09-02 13:10:54
收件人："namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>,"辛志宏" <xzhfood_at_njau.edu.cn>
主题：Re: namd-l: Wrong number of basis-sets stored!
Dear Zhihong,
Look in your qmBaseDir, where ORCA is writing intermediate files.
In your case, It is /dev/shm/NAMD_Example1
You should see a .TmpOut file which is written by ORCA for the current QM/MM step.
Since it is an ORCA specific error the TmpOut file may provide more details about the error.
One thing I did notice in your conf file that may raise some problem.
You specified to have 10 QM calculations while passing charge/multiplication information for only one qm region.
qmMult "1 2"
qmCharge "1 -1"
I assumed you have 10 qm regions since you requested:
# Number of simultaneous QM simulations per node
QMSimsPerNode 10
Best,
Atanu
On Sep 1, 2020, at 10:10 PM, 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
Deal Namd,
I came across a issue when I run a QM/MM simulation，
TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9.
[file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of basis-sets stored!
FATAL ERROR: Error reading QM forces file.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error reading QM forces file.
I do not find the solution in the mailing list and ask for help, any suggestion will be much appreciate.
My Namd config file as follows:
# This is a namd configuration file
## Single QM region with MM water box
structure ./ionized.psf
coordinates ./YZZ-namd-equil-last-1.pdb
# Continuing a job from the restart files
if {1} {
set inputname ../YZZ_equil_MM
binCoordinates $inputname.coor
#binVelocities $inputname.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.xsc
}
cellBasisVector1 64.945 0 0
cellBasisVector2 0 65.353 0
cellBasisVector3 0 0 67.919
cellOrigin 55.318 57.874 55.561
seed 7910881
# Output Parameters
binaryoutput no
outputname ./YZZ-QM-min-out
outputenergies 1
outputtiming 1
outputpressure 1
binaryrestart yes
dcdfile ./YZZ-QM-min-out.dcd
dcdfreq 1
XSTFreq 1
restartfreq 100
restartname ./YZZ-QM-min-out.restart
# mobile atom selection:
constraints on
consexp 2
consref ./YZZ-restraint.pdb
conskfile ./YZZ-restraint.pdb
conskcol B
constraintScaling 5.0
# PME Parameters
PME on
PMEGridspacing 1
set temperature 300
temperature $temperature
# Thermostat Parameters
langevin on
langevintemp $temperature
langevinHydrogen on
langevindamping 50
# Barostat Parameters
usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston on
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp $temperature
surfacetensiontarget 0.0
strainrate 0. 0. 0.
wrapAll on
wrapWater on
# Integrator Parameters
timestep 0.5
firstTimestep 0
fullElectFrequency 1
nonbondedfreq 1
# Force Field Parameters
paratypecharmm on
parameters ../CHARMpars/toppar_all36_carb_glycopeptide.str
parameters ../CHARMpars/toppar_water_ions_namd.str
parameters ../CHARMpars/toppar_all36_na_nad_ppi_gdp_gtp.str
parameters ../CHARMpars/par_all36_carb.prm
parameters ../CHARMpars/par_all36_cgenff.prm
parameters ../CHARMpars/par_all36_lipid.prm
parameters ../CHARMpars/par_all36_na.prm
parameters ../CHARMpars/par_all36_prot.prm
parameters ../common/DMP_ABD769.prm
#printExclusions on
exclude scaled1-4
1-4scaling 1.0
rigidbonds none
cutoff 12.0
pairlistdist 14.0
switching on
switchdist 10.0
stepspercycle 1
# Truns ON or OFF the QM calculations
qmForces on
qmParamPDB "./YZZ-namd-QM-0.pdb"
qmColumn "beta"
qmBondColumn "occ"
#Link Atoms
#qmBondDist on
#qmLinkElement
# Number of simultaneous QM simulations per node
QMSimsPerNode 10
QMElecEmbed on
QMSwitching on
QMSwitchingType shift
QMPointChargeScheme none
QMBondScheme "cs"
qmBaseDir "/dev/shm/NAMD_Example1"
## ORCA
qmConfigLine "! B3LYP 6-31G Grid4 PAL4 EnGrad TightSCF"
qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"
# construction of ORCA's input file.
qmMult "1 2"
qmCharge "1 -1"
qmSoftware "orca"
qmExecPath "/home/xzhfood/software/orca_4_1_2_linux_x86-64_openmpi313/orca"
QMOutStride 1
QMPositionOutStride 1
# Number of steps in the QM/MM simulation.
minimize 100
run 2000
Zhihong Xin
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST