[gmx-users] equilibrium

[Tamas Horvath]

sure... rmsd in itself is not very meaningful...

On 1/18/06, Lars Schaefer <Lars.Schaefer at mpi-bpc.mpg.de> wrote:
>
>
> 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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