**From:** dhacademic (*dhacademic_at_gmail.com*)

**Date:** Sun Nov 14 2010 - 09:51:40 CST

**Next message:**Peter Freddolino: "Re: pair interaction calculations"**Previous message:**jnsong: "the usage of ++nodelist and ++local"**Next in thread:**Peter Freddolino: "Re: pair interaction calculations"**Reply:**Peter Freddolino: "Re: pair interaction calculations"**Reply:**Axel Kohlmeyer: "Re: pair interaction calculations"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Everyone,

I want to calculate the interaction energy between two groups. The following

configuration file is used for the pair interaction calculation, and only

non-bonded terms are calculated. To make sure that the calculation is

correct, I also manually calculate the ELECT and VDW according to the

potential energy functions of namd (

http://www.ks.uiuc.edu/Research/namd/2.7/ug/node23.html). The system is very

simple, which only contains two Cl- (qi=qj=-1) with the distance of 3.57

angstrom (rij=3.57) in gas phase.

The results from the the following configuration file is 84.9920 (ELECT)

and 1.4148 (VDW). I can well reproduce the VDW result by manual calculation.

However, my manually calculated ELECT is 92.98, which is quite different

from the above result.

structure mycl.psf

paraTypeCharmm on

parameters par_all27_prot_lipid.prm

numsteps 1

exclude scaled1-4

outputname pair

temperature 0

COMmotion yes

cutoff 17

pairlistdist 18.5

dielectric 1.0

switchdist 15

pairInteraction on

pairInteractionGroup1 1

pairInteractionGroup2 2

pairInteractionFile mycl.pdb

pairInteractionSelf off

coordinates mycl.pdb

run 0

Any suggestion is appreciated,

Best,

Hao

**Next message:**Peter Freddolino: "Re: pair interaction calculations"**Previous message:**jnsong: "the usage of ++nodelist and ++local"**Next in thread:**Peter Freddolino: "Re: pair interaction calculations"**Reply:**Peter Freddolino: "Re: pair interaction calculations"**Reply:**Axel Kohlmeyer: "Re: pair interaction calculations"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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