From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Sat May 02 2020 - 05:30:42 CDT
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; BQ_BEGIN BQ_END
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