[gmx-users] equilibrium

[David Mobley]

This is a nontrivial question, and the answer partly depends on what you are
trying to do. As David points out, if you want to do protein folding, say,
your protein needs to have long enough to forget about its starting state
(hence his comment about folding and unfolding). Usually that takes a
prohibitively long time, though, for large proteins. So assuming you don't
want to solve the protein folding problem you have to be content with
something less. Definitely you want to run long enough that the protein RMSD
quits increasing, temperature and energy begin fluctuating around some
relatively stable value,  and so on. You can also look for things like
number of protein-water hydrogen bonds if you have explicit solvent; this
tends to take a much longer time to equilibrate.

Probably a good suggestion is to find out what other people have done who
are doing something similar to you, and make sure you equilibrate at least
as much as they do. :)

David


On 1/17/06, Tamas Horvath <hotafin at gmail.com> wrote:
>
> How may I check when a system reached it's equilibrium?
>
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