[gmx-users] equilibrium

[Lars Schaefer]

Hi Tamas,
just a remark about the rmsd with respect to the Xray structure: you 
might want to plot rmsd vs log(time), that is a better check sometimes.
Cheers,
Lars



Tamas Horvath wrote:

> I start from a quite valid folded state of the protein...
>
> On 1/17/06, *David Mobley* <dmobley at gmail.com 
> <mailto: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. :)
>
>     David
>
>
>     On 1/17/06, *Tamas Horvath* < hotafin at gmail.com
>     <mailto:hotafin at gmail.com>> wrote:
>
>         How may I check when a system reached it's equilibrium?
>
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