How to run for periodic boundary Conditions?

From: Snigdha Chakraborty (
Date: Wed Jul 20 2005 - 12:19:32 CDT

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


# 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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