[gmx-users] Free energy calculation, parallel or sequential lambda runs ?
steletch at jouy.inra.fr
Fri Dec 15 18:02:54 CET 2006
David Mobley a écrit :
>> 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.
> If you are doing slow growth, that is an entirely different thing from
> doing parallel or sequential lambda runs. Slow growth gradually
> changes lambda from 0 to 1 in a continuous manner over the course of a
> simulation and I don't recommend it unless you have a particular
> problem where this is the only way to do it or something. But
> generally it leads to Hamiltonian lag.
You are right, i was confusing both terms, of course i want to do
parallels runs, thus specifying each lambda.
This has both advantages of avoiding the Hamiltonian lag and saving
computer time (since i can run the 20 simulations in parallel instead of
Thanks a lot for your long and clear explanation about procedure and
time, it'll save some time for getting experience in the field :-)
I'll try to update my construction procedure (to be published soon) to
take your advices into account.
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
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