From: Oscar Bastidas (obastida_at_umn.edu)
Date: Sat May 02 2020 - 15:35:17 CDT
Thanks for your response Michael. What you're saying makes sense.
How about the restart coor, vel and xsc files? I believe these files were
generated in my failed runs and I thought that subsequent jobs appealed to
these files, not the dcd file. Furthermore, I thought the dcd file was
only created when a snapshot moment had finally been reached in the
calculations and that the above restart coor, vel and xsc files maintained
track of when such snapshot moment had become necessary. I guess I was
wrong in thinking that!
My initial goal for what I am trying to do is a design of experiments (DOE,
statistical definition) and I am trying to map out my experimental
operating space. One of the bordering conditions is this system that blew
up (and why I wrote for help): 800 nanoseconds and print out a total of 2
snapshots. Again, I'm not actually trying to do dynamics here for the sake
of studying the protein, but just probe this "extreme" simulation condition
for my DOE setup.
Thanks again.
Oscar B.
On Sat, May 2, 2020, 8:15 AM Michael Robinson <michael.robinson1_at_monash.edu>
wrote:
> Hi Oscar,
>
> Your simulation runs for 6,250,000 steps, and your DCD output frequency
> is every 200,000,000 steps - this means an output is never generated. The
> same is true for your xst output, as well as energies and timings. These
> will need to be at least set to a value lower than 6,250,000 for output to
> occur - given a timestep of 2fs, an output frequency of 5000 will involve
> output every 10,000 fs (10ps), which is often fairly reasonable.
> Fundamentally it depends on the timescale of the processes you're
> interested in - with the job only running for 6,250,000 steps, you could
> have an output frequency of 1000 (2ps) and still not generate excessively
> large output files.
>
> Regards,
> Michael Robinson
>
> On Sat, 2 May 2020 at 20:36, Oscar Bastidas <obastida_at_umn.edu> wrote:
>
>> 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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