DCD File Not Generating

From: Oscar Bastidas (obastida_at_umn.edu)
Date: Sat May 02 2020 - 05:08:10 CDT


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.


Oscar B.
structure step3_charmm2namd.psf
coordinates step3_charmm2namd.pdb

                                                  set temp

set outputname snapshot-1;

#read system values written by CHARMM (need to convert uppercases to
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;


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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