AW: Letzte Hilfe

From: Norman Geist (
Date: Mon Aug 15 2011 - 07:16:39 CDT

Just consult the manaul for the parameter “velocities”. You need to remove
the setting for the initial temperature then like “temperature 310” because
you will already read it from the velocity restart.
Mit freundlichen Grüßen
Norman Geist.
Von: Babban Mia []
Gesendet: Montag, 15. August 2011 12:00
An: Norman Geist
Betreff: Letzte Hilfe
Hallo Norman

I normally prefer python over shell when it comes to writing text files.I am
very thankful to you for giving me the suggestions.
I still have one small doubt though

I use the following python script to write my .config file for firsttime
step run : and through a shell script,I plan to be writing the
further.namd/,config file to be used for further time steps.

f1.write('structure fullprotein.psf \n')
f1.write('coordinates fullprotein.pdb \n')

f1.write('set temperature 310 \n')

f1.write('set outputname protein \n')

f1.write('firsttimestep 0 \n')

f1.write('paraTypeCharmm on \n')
f1.write('parameters par_all27_prot_lipid.inp \n')

f1.write('temperature 310 \n')

f1.write('exclude scaled1-4 \n')

f1.write('1-4scaling 1.0 \n')

f1.write('cutoff 12.0 \n')

f1.write('switching on \n')

f1.write('switchdist 10.0 \n')

f1.write('pairlistdist 14.0 \n')

f1.write('timestep 2.0 \n')

f1.write('rigidBonds all \n')

f1.write('nonbondedFreq 1 \n')

f1.write('fullElectFrequency 2 \n')

f1.write('stepspercycle 10 \n')

f1.write('langevin on \n')

f1.write('langevinDamping 1 \n')

f1.write('langevinTemp 310 \n')

f1.write('langevinHydrogen off \n')

f1.write('cellBasisVector1 40.0 0.0 0.0 \n')

f1.write('cellBasisVector2 0.0 40.0 0.0 \n')

f1.write('cellBasisVector3 0.0 0.0 40.0 \n')

f1.write('cellOrigin 0.0 0.0 0.0 \n')

f1.write('wrapAll on \n')

f1.write('PME yes \n')

f1.write('PMEGridSpacing 1.0 \n')
f1.write('#manual grid definition \n')
f1.write('#PMEGridSizeX 45 \n')
f1.write('#PMEGridSizeY 45 \n')
f1.write('#PMEGridSizeZ 48 \n')
f1.write('useGroupPressure yes \n')

f1.write('useFlexibleCell no \n')

f1.write('useConstantArea no \n')

f1.write('langevinPiston on \n')

f1.write('langevinPistonTarget 1.01325 \n')

f1.write('langevinPistonPeriod 100.0 \n')

f1.write('langevinPistonDecay 50.0 \n')

f1.write('langevinPistonTemp 310 \n')

f1.write('outputName fullprotein1 \n')
f1.write('binaryoutput no \n')
f1.write('restartfreq 500 \n')

f1.write('dcdfreq 250 \n')

f1.write('xstFreq 250 \n')

f1.write('outputEnergies 100 \n')

f1.write('outputPressure 100 \n')

f1.write('minimize 500 \n')

f1.write('reinitvels 310 \n')

f1.write('run 2500 \n')

As you can see above,I have set the temperature for Thermostat and
everything but I guess this is appropriate for the first run,for the
subsequent run ,I would need not specify the temperature again instead read
in the veleocities from .vel file.

My doubt is ,What changes would be required for the above file to run it
beyond the first time step. I am sure I need not specify the periodic
boundary condities,langevin piston etc. Please advise me one last time.Can
you write those changes for me as a response to this mail ?

Ich bin sehr dankbar für die Ratschläge


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