**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Sun Nov 14 2010 - 11:58:19 CST

**Next message:**dhacademic: "Re: pair interaction calculations"**Previous message:**Peter Freddolino: "Re: pair interaction calculations"**In reply to:**dhacademic: "pair interaction calculations"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

*> Hi Everyone,
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*>
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*> I want to calculate the interaction energy between two groups. The following
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*> configuration file is used for the pair interaction calculation, and only
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*> non-bonded terms are calculated. To make sure that the calculation is
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*> correct, I also manually calculate the ELECT and VDW according to the
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*> 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 calculation.
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*> However, my manually calculated ELECT is 92.98, which is quite different
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*> from the above result.
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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.

*>
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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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*>
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*> Best,
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*> 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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