AMBER Archive (2004)

Subject: Re: AMBER: sander_classic for cap simulations?

From: David A. Case (
Date: Mon May 17 2004 - 15:18:41 CDT

On Thu, May 13, 2004, Oliver Hucke wrote:
> I recently posted a message about the large fuctuations of the
> electrostatic energy observed with a system with a solvent cap and
> sander of amber8 with a non-infinite non-bonded cutoff.
> After a reply from Ben Cossins I used sander_classic (of amber6) for the
> same simulations in order to make use of a residue based instead of an
> atom based non-bonded cutoff. The fluctuations are much smaller and the
> system seems to equilibrate.

This is unusual. It is generally thought that atom-based truncation is
(counter-inutitively) better than residue-based truncation for aqueous
systems, and the both are worse than PME. Please also keep in mind the points
made last week by Tom Cheatham:

> Is it possible to use a residue based cutoff with sander of amber8?


> Or is the usage of sander_classic for simulations with a cap still the
> way to go?
> If so, should sander_classic not be part of the amber8 distribution?

There are certain types of calculations that are still faster or more
convenient with sander_classic, and the developers do keep in mind user
requests. It is often a matter of finding someone being willing to do the
work of supporting and developing a particular code.



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to