Ignacio Fernández Galván a écrit :
--- David Mobley <[EMAIL PROTECTED]> 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
input
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
a
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.
Ignacio
Thanks for your answer,
Cheers,
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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