[gmx-users] Free energy calculation, parallel or sequential lambda runs ?
steletch at jouy.inra.fr
Fri Dec 15 18:09:50 CET 2006
Ignacio Fernández Galván a écrit :
> --- David Mobley <dmobley at gmail.com> wrote:
>> In terms of implementation, what I do is I prepare a particular
>> equiliibrated structure of my system in water. Then I set up run
>> files for all of my different lambda values, and I then minimize and
>> equilibrate my system AGAIN at each different lambda value, so now I
>> have nlambda different equilibrated structures, each appropriate for
>> different lambda value. I then run production beginning with each of
>> these structures.
> OK, I do basically the same, but instead of starting the second
> equilibration from the same structure for each lambda, I start from the
> final structure of the previous lambda (still, I equilibrate before
> production for each lambda). I don't see why this strategy should be
> worse the one you outlined, unless there was something strange/bad
> happening at some lambda value, which is already bad on itself.
> Granted, there is the obvious advantage of parallel runs, but when you
> only have one computer this is unimportant (and maybe with the
> "sequential" run you can go with shorter equilibrations).
My confusion was coming from the slow growth versus fixed lambda/ In
your case, i presume you're somewhere in the middle of both methods
since you link all dynamics (even not explicitly, but i presume this ie
nearly a slw-growth like method).
For running the FEP using n lambdas, i presume, one specifies delta_lamba=0.
For slow-growth, i presume delta_lambda is small but different from 0.
> Am I missing anything? When you talk about "sequential" run, do you
> mean no equilibration for each lambda? (there I do see a problem).
No, using equilibration between each lambda, but i was mixing both cases.
Thanks for your answer,
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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