Electrostatics energy calculation

From: Ben Roberts (Ben.P.Roberts_at_vcp.monash.edu.au)
Date: Wed May 26 2004 - 20:09:43 CDT

Hello all,

In order to verify that NAMD is ideal for some dynamics simulations that I
wanted to do, I am currently comparing it against the Gromacs and Tinker

This is using the OPLS forcefield, and modified so that Van der Waals
interactions (Lennard-Jones) are calculated using geometric rather than
arithmetic means.

I find that when I do an energy calculation on n-Butane in an arbitrary
initial conformation that is nevertheless close to the fully anti
conformation, I get the following results:

Property Gromacs Tinker NAMD

Bonds 0.8760 0.8760 0.8760
Angles 0.3034 0.3034 0.3034
Dihedrals 0.0039 0.0042 0.0039
Impropers 0.0000 0.0000 0.0000
Van der Waals -0.1146 -0.1145 -0.1145
Electrostatics 1.9024 1.9024 1.5451
Total 2.9712 2.9714 2.6138

As the above results show, most of the energies work out to be almost
identical. The exception is the electrostatics.

Does anyone have any idea why the electrostatics would be so different
when everything else is the same?

I have checked that the individual atom coordinates are the same - and
this would affect other things if any were wrong anyway; and the partial
charges on the individual atoms are also the same.

In all simulations, I am using scaled 1-4 interactions, and PME is turned

Any help appreciated. Thanks in advance.

Best regards,

Benjamin P. Roberts, B.Sc.(Hons)
Ph.D. Student

Department of Medicinal Chemistry
Victorian College of Pharmacy (Monash University)
381 Royal Parade, Parkville VIC 3052, Australia

Phone +61 3 9903 9674 | Fax +61 3 9903 9582 | Mobile +61 401 784 940

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