Effect of FullDirect electrostatics

From: Ben Roberts (Ben.P.Roberts_at_vcp.monash.edu.au)
Date: Mon May 31 2004 - 18:22:45 CDT

Hi all,

When trying to test NAMD on small molecules, I ran across FullDirect
electrostatics as having a very significant effect.

I had noticed a smaller error in the electrostatics in n-butane, so I
tested it on two Cl- ions which were close together in space but had no
bonding interactions connecting them.

The results I found were as follows:

FullDirect OFF: Electrostatic energy is 87.4571 kcal/mole

FullDirect ON: Electrostatic energy is 110.6879 kcal/mole

This second answer (with FullDirect ON) agrees closely with that
calculated from the TINKER package (110.6846) and with a direct
calculation (110.6635).

I note that NAMD defaults to FullDirect being OFF. This looks like it
can create a significant difference. Is this actually OK, and if so, how?


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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