From: Hasan haska (hasanhaska_at_yahoo.com)
Date: Tue Dec 13 2011 - 08:10:49 CST
Dear Namd
Users,
I run 5 ns
md simulation for water molecules with the conf file below. And I want to get
the final coordinates of all water molecules in defined cell sizes ( 40 40 65 ) . How can I do
this operation in NAMD ?
Thank you
very much for your help.
Regards.
*********
#--- This is a test namd configuration file
paratypeCharmm on
parameters water.prm
structure water.psf
coordinates water.pdb
outputName water_1out
set temperature 300
temperature $temperature
firsttimestep 0
# Integrator Parameters
timestep 1
nonbondedFreq 1
fullElectFrequency 5
stepspercycle 10
# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.8333333
cutoff 19.7
switching on
switchdist 17
pairlistdist 24
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen on ;# don't couple langevin bath to hydrogens
#--- PBC
cellBasisVector1 40. 0.0 0.0
cellBasisVector2 0.0 40. 0.0
cellBasisVector3 0.0 0.0 65.
#--- PME
dielectric 1
PME on
PMEGridSizeX 45
PMEGridSizeY 45
PMEGridSizeZ 72
# Constant Preswaterre Control (variable volume)
useGroupPressure no
useFlexibleCell yes
useConstantArea yes
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature
#--- Output & Restart
binaryoutput no
binaryrestart yes
restartname water_restart
DCDfile water_out.dcd
restartfreq 1250
dcdfreq 1250
xstFreq 1250
outputEnergies 1250
forceDCDfreq 1250
outputPressure 1250
outputtiming 1250
minimize 12500
reinitvels $temperature
run 5000000
*************
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