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
--
==================================================================
David A. Case | e-mail: case.scripps.edu
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 | http://www.scripps.edu/case
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Received on Mon May 17 2004 - 21:53:00 PDT
