Re: your mail

From: David A. Case <>
Date: Thu, 10 Jul 2003 20:01:51 -0700

On Wed, Jul 09, 2003, Richard Dayton Smith wrote:
> I am working with a large solvated system, (approximately 50000 atoms),
> and I am performing a Free Energy Perturbation Calculation which
> changes the system from a net neutral to an overall -1 charge. I would
> like to use PME to help speed up the calculation in Gibbs, since the
> system is so big. I notice in the AMBER6 manual that using PME in Gibbs
> is experimental. Has this been tested, and can PME be used with Gibbs
> and still produce a reliable result? Also, if it could be used, could
> the new PMEMD program be incorporated into a Gibbs calculation to
> improve efficiency?

You first concern in free energy should be accuracy and reliability, not
efficiency. Having said that, all of the PME things that gibbs could do can
be done equally well (and faster) in sander, so that is what I would
recommend. But if at all possible, you should consider upgrading to version

You can use Gibbs PME (there is nothing wrong with it)...note that it is
limited to thermodynamic integration calculations. That is a good choice
for most, but not all, types of perturbations.

...good luck...dac

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            |
Received on Fri Jul 11 2003 - 04:53:01 PDT
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