Re: water models supported in NAMD

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Wed Feb 06 2008 - 14:14:27 CST

Philip Peartree wrote:

> I would imagine that would be a forcefield problem, so I guess you'd
> have to ask either the charmm guys (alex mckerell et al) or the AMBER
> guys, although I'm not sure.

It's not necessarily a "force field" problem, it's more of an
implementation problem. SPC and SPC/E force fields are easy to put into
NAMD, since they have charges centered on atomic sites. TIP4P is a
problem because it has a 4th charge that is on the bisector of the H-O-H
angle, and is not on the oxygen atom. That causes a lot of trouble when
you try and make it work in NAMD. I built TIP4P water fine, but I
needed to use a very small timestep (0.1-0.2 fs) or the simulation would
blow up. I tried a number of different fictious masses for the lone
charge without much success. I also tried to make the molecule
completely rigid. I tried flexible, and varying degrees of
flexibility. Still couldn't make the simulation stable with a 1fs
timestep. What would be helpful if someone could explain why having
charges off the atomic sites results in such unstable behavior.

Regards,
    Jeff

-- 
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Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
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