Re: pair interaction calculations

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Nov 14 2010 - 11:58:19 CST

On Sun, Nov 14, 2010 at 10:51 AM, dhacademic <dhacademic_at_gmail.com> wrote:
> 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.

you didn't say anything about how your input treats long-range
electrostatics. if you have PME enabled, then your real-space
coulomb interactions will be damped.

axel.

>
> 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

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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