Re: pair interaction calculations

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Nov 14 2010 - 11:56:25 CST

Did you properly account for the shifting function
(http://www.ks.uiuc.edu/Research/namd/2.6/ug/node24.html#SECTION00081200000000000000)
in your manual calculation? N.b. unlike the vdw interaction, if you have
PME off the electrostatic energies/forces will be affected at all
distances, not just past the switching distance.
Best,
Peter

On 11/14/2010 10:51 AM, dhacademic 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.
>
> 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

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