pair interaction of water molecules

From: divya nayar (divya.alchemist_at_gmail.com)
Date: Wed Nov 24 2010 - 03:41:13 CST

hi,
I am doing a simulation of 256 water molecules in a cubic box. I want to
find the pair interaction energy between two water molecules in this system.
In order to check the values I want to check the van der Waal's component of
pair interaction energy by manually calculating. I want to ask whther NAMD
uses just the LJ potential to calculate the vdW component. I mean are there
any other parameters which NAMD takes into account. I read user's guide. In
the manual, it just says the LJ potential. My manually calculated values are
not matching with those from simulations. My conf file looks like as
follows:

structure ../../tip4p.psf
coordinates ../../tip4p-prod260.coor

set outputname 4tip.tpe

temperature 260
seed 4010

paraTypeCharmm on
#parameters ../par_all27_prot_lipid.inp
parameters ../../tip4p.par

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
dielectric 1.0
cutoff 9.5
switching on
switchdist 7.5
pairlistdist 11.5
margin 0.0
# Integrator Parameters
timestep 1.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
rigidTolerance 0.00001
rigidIterations 100
wrapAll on
wrapWater on

waterModel tip4
# Periodic Boundary Conditions
PME yes
PMETolerance 0.000001
PMEGridSizeX 40
PMEGridSizeY 40
PMEGridSizeZ 40

# Output
outputName $outputname
outputTiming 500
extendedSystem ../../tip4p-prod260.xsc

pairInteraction on
pairInteractionFile ../pdb/abc.pdb
pairInteractionCol B
pairInteractionGroup1 1
pairInteractionGroup2 2
#############################################################
## EXECUTION SCRIPT ##
#############################################################
set ts 100

coorfile open dcd ../8000.dcd

while {! [coorfile read] } {
   firstTimestep $ts
   run 0
   incr ts 100
}

coorfile close

While calculating the pair interaction between water molecules, does NAMD
use center of mass of water for coordinates (coordinates of oxygen)? Because
I am using the coordinates of oxygens to do manual calculation.
can anyone help me with this?

Thanks,
Divya

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