From: dhacademic (dhacademic_at_gmail.com)
Date: Sun Nov 14 2010 - 17:42:59 CST
Hi Peter,
Thanks for the comment. With the shifting function included, I can reproduce
the value of ELECT very well. Many thanks!
Best,
Hao
On Sun, Nov 14, 2010 at 12:56 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:
> 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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