**From:** Peter Freddolino (*petefred_at_ks.uiuc.edu*)

**Date:** Sun Nov 14 2010 - 11:56:25 CST

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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
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*> following configuration file is used for the pair interaction
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*> calculation, and only non-bonded terms are calculated. To make sure that
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*> the calculation is correct, I also manually calculate the ELECT and VDW
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*> according to the potential energy functions of namd
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*> (http://www.ks.uiuc.edu/Research/namd/2.7/ug/node23.html). The system is
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*> very simple, which only contains two Cl- (qi=qj=-1) with the distance of
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*> 3.57 angstrom (rij=3.57) in gas phase.
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*>
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*> The results from the the following configuration file is 84.9920 (ELECT)
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*> and 1.4148 (VDW). I can well reproduce the VDW result by manual
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*> calculation. However, my manually calculated ELECT is 92.98, which is
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*> quite different from the above result.
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*>
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*> structure mycl.psf
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*> paraTypeCharmm on
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*> parameters par_all27_prot_lipid.prm
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*> numsteps 1
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*> exclude scaled1-4
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*> outputname pair
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*> temperature 0
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*> COMmotion yes
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*> cutoff 17
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*> pairlistdist 18.5
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*> dielectric 1.0
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*> switchdist 15
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*> pairInteraction on
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*> pairInteractionGroup1 1
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*> pairInteractionGroup2 2
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*> pairInteractionFile mycl.pdb
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*> pairInteractionSelf off
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*> coordinates mycl.pdb
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*> run 0
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*>
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*> Any suggestion is appreciated,
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*>
*

*> Best,
*

*> Hao
*

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