From: Oscar Bastidas (obastida_at_umn.edu)
Date: Sat May 02 2020 - 05:31:03 CDT
Awesome. Would you happen to know what is an acceptable dcd frequency
size? Thanks.
Oscar
Oscar B.
On Sat, May 2, 2020, 5:31 AM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
wrote:
> Dear friend,
> Clearly, the dcd frequency is tooooooo large.
>
> *--*
> *All the best,*
> *Ashkan Shekaari,*
> *Ph.D Candidate in Solid State Physics,*
> *K. N. Toosi University of Technology,*
> *Tehran, Iran*
>
> ------------------------------
> *From: *"Oscar Bastidas" <obastida_at_umn.edu>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu>
> *Sent: *Saturday, May 2, 2020 2:38:10 PM
> *Subject: *namd-l: DCD File Not Generating
>
> Hello,
>
> I am trying to run my simulations and my dcd files are never generated. I
> can't figure out why it's not working when this is something that has
> worked in the past for previous simulations/jobs. Furthermore, my cluster
> system indicates that the NAMD job terminated normally.
>
> The entire simulation is supposed to be several back to back simulations,
> but my first simulation never generates a dcd file. The log file even says
> that the coordinate dcd file was not created.
>
> Everything looks normal in my conf file as I've always had it for previous
> successful runs and I get no error files generated either. Could someone
> please offer me insight as to why no dcd file is ever being created? What
> could be causing this?
>
> I am using CHARMM-GUI to generate my simulation package.
>
> My conf file contents are below the line of asterisks.
>
> Thanks.
>
> Oscar B.
> ************************************************************************
> structure step3_charmm2namd.psf
> coordinates step3_charmm2namd.pdb
>
> set temp
> 310.15;
>
> set outputname snapshot-1;
>
> #read system values written by CHARMM (need to convert uppercases to
> lowercases)
> exec tr "\[:upper:\]" "\[:lower:\]" < ../step3_pbcsetup.str | sed -e "s/
> =//g" > step3_charmm2namd.str
>
> source step3_charmm2namd.str
>
> temperature $temp;
>
> outputName $outputname;
>
> firsttimestep 0;
>
> restartfreq 200000000;
>
> dcdfreq 200000000;
> dcdUnitCell yes;
> xstFreq 200000000;
> outputEnergies 200000000;
> outputTiming 200000000;
>
> paraTypeCharmm on;
>
> <PARAMETER LIST ...>
>
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> vdwForceSwitching yes;
> # You have some freedom choosing the cutoff
> cutoff 12.0;
> switchdist 10.0;
> pairlistdist 16.0;
> stepspercycle 20;
> pairlistsPerCycle 2;
>
> #Integrator Parameters
> timestep 2.0;
> rigidBonds all;
> nonbondedFreq 1;
> fullElectFrequency 1;
>
> # Constant Temperature Control ONLY DURING EQUILB
> reassignFreq 500;
> reassignTemp $temp;
>
> # Periodic Boundary conditions. Need this since for a start...
> cellBasisVector1 $a 0.0 0.0;
> cellBasisVector2 0.0 $b 0.0;
> cellBasisVector3 0.0 0.0 $c;
> cellOrigin 0.0 0.0 $zcen;
>
> wrapWater on;
> wrapAll on;
> wrapNearest off;
>
> # PME (for full-system periodic electrostatics)
> PME yes;
> PMEInterpOrder 6;
> PMEGridSpacing 1.0;
>
> # Pressure and volume control
> useGroupPressure yes;
>
> useFlexibleCell no;
> useConstantRatio no;
>
> langevin on
> langevinDamping 1.0
> langevinTemp $temp
> langevinHydrogen off
>
> # constant pressure
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 50.0
> langevinPistonDecay 25.0
> langevinPistonTemp $temp
>
> # constraints on
> # consexp 2
> # consref restraints/prot_posres.ref
> # conskfile restraints/prot_posres.ref
> # conskcol B
> # constraintScaling 1.0
>
> minimize 10000
> # numsteps 90000000
> run 6250000;
>
>>
>
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