From: Oscar Bastidas (obastida_at_umn.edu)
Date: Sat May 02 2020 - 15:50:36 CDT
Hello Josh,
Thanks for this insight and yes, what you're saying makes perfect sense.
As I responded to another researcher who also reached out, I had thought
that the restart coor, vel and xsc files (which did print out if I recall
correctly) kept track of when a dcd file needed to be populated and that
consequently my future back-to-back jobs would just continue running with
input from the above restart coor, vel and xsc files only (as specified in
downstream conf files), and that when the time came to finally print
out/generate the dcd file, that trigger would be established by those
restart files.
Finally, my goal here was to establish an experimental operating space for
a design of experiments and I need to consequently probe this "extreme"
simulation condition of 800 nanoseconds printing out a total of 2 snapshots.
Apparently, since the first dcd file never printed, my subsequent
downstream continuation simulations never yielded anything, not even the
above restart files.
Thanks again for your response.
Oscar B.
On Sat, May 2, 2020, 10:12 AM Josh Vermaas <joshua.vermaas_at_gmail.com> wrote:
> You are running 90 million steps with a dcdfreq of 200 million. NAMD
> didn't reach step 200 million, and so it didn't write a dcd. That probably
> wasn't what you intended. I usually use a dcdfreq of 5000, so I get a frame
> every 10ps of simulation time.
> Josh
>
> On Sat, May 2, 2020, 4:12 AM Oscar Bastidas <obastida_at_umn.edu> wrote:
>
>> 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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