David Mobley a écrit :
Stéphane,
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
serial).
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.
Best wishes,
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
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