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?

Thanks
Ben

----------------------------------------------------------------------
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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