AMBER Archive (2003)

Subject: Re: AMBER: length of deltaG calcs

From: David Smith (David.Smith_at_cup.uni-muenchen.de)
Date: Mon Dec 15 2003 - 10:16:26 CST

Hi Heather,

I guess the answer that most people would give is that it depends on the
form of the perturbation and how many windows you plan to use.

If you're planning on using thermodynamic integration (TI) rather than
FEP itself (which I personally would recommend) , you can relatively
easily monitor the convergence behavior of <dV/dLam>Lam (the ensemble
average of the derivative at a particular value of lamda) to see how
long you should simulate a given "window".

You can also do something similar with FEP but its a bit simpler with
TI.

How you do this depends on whether you want to use sander or gibbs but
if this approach interests you and you need more info, just holler.

Good Luck.

David.

On Mon, 2003-12-15 at 16:32, Heather A.Carlson wrote:
> Hi Everyone,
>
> We're starting a series of FEP calcs in my lab. My hands-on experiences
> with FEP involved Monte Carlo simulations which don't directly translate
> into a given length of MD. I am wondering what the current range is for
> averaging in each window? I've seen 10ps eq + 30ps ave in the literature,
> but that sounds short to me. 1 ns per window would take too long for our
> project.
>
> Thank you, Heather
> _________________________________________________________________________
> "Black holes are where God divided by zero" Steven Wright
>
> Heather A. Carlson, Ph.D.
> John Gideon Searle Assistant Professor of Medicinal Chemistry
> Assistant Professor of Chemistry
> Affiliated Faculty, Biophysics Research Division
> Affiliated Faculty, Bioinformatics Program
>
> http://www.umich.edu/~pharmacy/MedChem/faculty/carlson/
>
> University of Michigan Phone: (734) 615-6841
> College of Pharmacy (2555 CCL) FAX: (734) 763-2022
> 428 Church Street E-mail: carlsonh_at_umich.edu
> Ann Arbor, MI 48109-1065
> _________________________________________________________________________
>
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-- 
---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 77740
Fax.: +49 (0)89 2180 77738
e-mail: David.Smith_at_cup.uni-muenchen.de
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