AMBER Archive (2003)

Subject: Re: Gibbs, ewald and ifc

From: David A. Case (case_at_scripps.edu)
Date: Fri Jan 31 2003 - 15:56:25 CST

On Fri, Jan 31, 2003, David Smith wrote:
>
>
> At the moment I am trying to do a few things with gibbs in a large periodic
> system for which I would like to use ewald. As far as I can tell, the things
> I am trying to do require some particular features of gibbs (PMFs,
> contributions of constraints etc.) so that I cannot use sander from amber7. I
> have been managing OK up unitl now with the amber6 version of gibbs compiled
> with either g77 or pgf77.

Note that the *only* thing that gibbs + PME supports is thermodynamic
integration. Unfortunately, you can't combine the PMF and constraint
capabilities of gibbs with its PME capabilities.

In version 7, we turned off the PME option in gibbs, since everything that
was supported there is now in sander.

>
> I gave the amber7 distribution a go with -DEWALD and it seems to work (not
> extensively tested at this stage but I get an executable).

It will probably "work" (as in Amber 6), but the PME facility in gibbs is an
old implementation, and does not have any of the improvements made over the
past 8 years or so. In particular, it is not quite as accurate, does not
conserve energy as well, and does not contain the long-range van der Waals
correction (which is often important in free energy simulations.) So
basically, for the reasons outlined above, we don't recommend using Ewald with
gibbs.

My personal view is this: most conformational free energy calculations (e.g.
PMF's) should be done with umbrella sampling; and most "alchemical" changes
should be done with thermodynamic integration. Given our limited resources,
these are the items that we are concentrating on as Amber goes forward.

If you don't need the Ewald part, then gibbs provides a platform for carrying
out a large variety of free energy calculations. But it's definitely
not for the faint of heart...everyone should be sure to study the manual
carefully, and to run short trial simulations to be sure that the program is
doing what is intended.

..good luck....dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_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
==================================================================