AMBER Archive (2004)

Subject: Re: AMBER: sander_classic for cap simulations?

From: David A. Case (case_at_scripps.edu)
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:
        http://amber.ch.ic.ac.uk/archive/200405/0153.html

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

No.

> 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.

...regards...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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