[gmx-users] Free energy calculation, parallel or sequential lambda runs ?

[Stéphane Téletchéa]

Dear colleagues,

I'm willing to do some FEP using the slow groth approach available in 
gromacs (as of 3.3.1). While retrieving articles and the mailing list, i 
found out there where arguments against sequential runs (particularly 
for avoiding the hysteresis problem), and other against parallel runs.

I would greatly appreciate your opinion about running a parallel (double 
precision) or sequential procedure (with 20 lambdas for 200ps of 
equilibration and 300 ps of 'production' for each lambda), and if 
possible some pointers towards documentation (i've read the manual, the 
Dill's group tutorial, the chapter from Leach, and some other 
publication from Aqvist, but still i'm not completely convinced of the 
procedure).

Yours,

Stéphane
-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901