[gmx-users] equilibrium

[Lars Schaefer]

well, rmsd is not that bad. Just that it is easier to judge a converged 
rmsd from a non-converged one when you plot it against log(t) instead of t.
Another convergence check is the cosine content of the traj projected 
onto some (slow) PCA modes.
Cheers,
Lars

Tamas Horvath wrote:

> sure... rmsd in itself is not very meaningful...
>
> On 1/18/06, *Lars Schaefer* <Lars.Schaefer at mpi-bpc.mpg.de 
> <mailto: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>
>     > <mailto: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>
>     >     <mailto: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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