hotafin at gmail.com
Tue Jan 17 22:34:15 CET 2006
I start from a quite valid folded state of the protein...
On 1/17/06, David Mobley <dmobley at gmail.com> wrote:
> 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. :)
> 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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