Re: water models supported in NAMD

From: Jeffrey J. Potoff (
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.


Jeffrey J. Potoff               
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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:14 CST