[gmx-users] Simulated Annealing

[Dr. Christoph Freudenberger]

Hi Martina,

Martina Bertsch, PhD wrote:
> My questions are:
> 
> a) Is there a way to program the whole protocol in a single mdp? Which 
> mdp options do I use?
As David pointed already out there is no direct way
to do it. AFAIC the best solution is to provide a
mdp for each step and to use some shell scripts to
have them executed sequentially.

> In the past, I used a simple SA cooling from 600 to 0 K in 1 ns (see 
> enclosed mdp), but the papers suggest that a more gradual cooling is 
> preferred.
Which papers are you refenecing to, acctually?

regards
-- 
------------------------------------------------
Dr. Christoph Freudenberger
Institut fuer Organische Chemie and Biochemie II
Technische Universitaet Muenchen
Lichtenbergstr. 4
D-85747 Garching, Germany

Tel.: ++49 (0)89 289 13313
Fax.: ++49 (0)89 289 13210
email: Christoph.Freudenberger at ch.tum.de
------------------------------------------------