From: Snigdha Chakraborty (snigdha_chakraborty123_at_yahoo.com)
Date: Wed Jul 20 2005 - 12:19:32 CDT
Hello,
I have just started the NAMD 2.5 package.I have started for a simple compound called ethane.
I have written the pdb,psf and parameter file for it.
The config file is as written below
I want to calculate the Molar volume,cohesive energy density and other measurable properties for such a compound.This i can only do with a PBC .Suppose i want to put 100 molecules of ethane in the cell please tell me how i should modify the config file.
Presently the ouptut i am getting are the different forms of energies and temperture
thanks
snigdha
...............................
# NAMD CONFIGURATION FILE FOR ETHANE
# protocol params
numsteps 1000
# initial config
coordinates ethane.pdb
temperature 300K
seed 12345
# output params
outputname /tmp/ethane
binaryoutput no
# integrator params
timestep 1.0
rigidbonds all
nonbondedFreq 1
fullElectFrequency 2
# force field params
structure ethane.psf
parameters ethane.params
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 20
# Constant Pressure Control
useGroupPressure yes
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