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.
> 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,
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:21 CST