AMBER Archive (2003)

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

From: Yong Duan (yduan_at_udel.edu)
Date: Sat Jul 05 2003 - 13:48:01 CDT

Just to follow-up what Carlos was saying,

In AMBER, SHAKE is parallelized for H- atoms only. So, once you invoke
SHAKE you can constrain bonds with H atoms on parallel platforms. This
rule does not apply to single-CPU platforms. In the later case, you can
use SHAKE to constrain all bonds (ITC=3?).

Assume you use parallel platforms, if only the bonds connecting to H
atoms are rigid in you solvent model, you are ok. Just set ITC=2. In
case, other bonds are also required to be rigid, you can "fake" the H
atoms. I tried couple of times, SANDER did not really know the
difference. Of course, this can be confusing to a third party who
happens to look at your PDBs and you may need to write a script to
convert the atom names back. In the end, we probably should make it more
flexible to allow users to specify a list of atoms whose bonds are to be
constrained.

yong
-----Original Message-----
From: Carlos Simmerling [mailto:carlos_at_csb.sunysb.edu]
Sent: Friday, July 04, 2003 1:25 PM
To: Marco Aurelio Correia Preto
Cc: amber_at_heimdal.compchem.ucsf.edu
Subject: Re: How to do a rigid solvent model?

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?
> >
>