pair interaction energy for 2 water molecules

From: divya nayar (divya.alchemist_at_gmail.com)
Date: Mon Nov 29 2010 - 04:00:14 CST

Hi,
I want to calculate the pair interaction energy between 2 water molecules in
a system of 256 waters. My conf file is below.
I am able to reproduce the van der Waal's component of pair interaction
energy by manual calculations using LJ potential defined in User's guide. I
want to ask how should I change my PME parameters to tell NAMD to calculate
the electrostatic energy between only those two tagged water molecules in a
system of 256 water molecules because the electrostatic energy for 2
molecules that I am getting is not very much different from that of between
one molecule interacting with all other 255 molecules.
Also, is there a way I can check the values tht I am getting for
electrostatic energy are correct?
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

Please guide me. Thanks in advance

Divya

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