AMBER Archive (2003)

Subject: Re: How to do a rigid solvent model?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Jul 04 2003 - 12:25:21 CDT

Large force constants are not a good idea-
they increase the frquency of the motion and
thus require smaller time steps for stable
MD simulation. The TIP3P water used in AMBER
is kept rigid by SHAKE, you might want to try
something similar.

> On Fri, Jul 04, 2003, Marco Aurelio Correia Preto wrote:
> >
> > We are doing some molecular dynamic runs of small non-standart peptides
(in
> > water) and we would like to do the smae dynamics in other solvents!
There
> > are a couple of potential for organic solvents, but some of them are
rigid
> > one! How can we do this in Amber (version 6 is the one we have)? Can we
use
> > very large force constants to force a rigid conformation?
> >
>