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

Ignacio Fernández Galván jellby at yahoo.com
Fri Dec 15 17:47:42 CET 2006

--- 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
> 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).

Am I missing anything? When you talk about "sequential" run, do you
mean no equilibration for each lambda? (there I do see a problem).


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