[gmx-users] Saving time of the coordinates for conformational entropy

[Tsjerk Wassenaar]

Hi Qasim,

The RMSD is not good for assessing convergence, especially if it goes above
0.5 nm.

Cheers,

Tsjerk


On Wed, Jun 8, 2016 at 8:48 PM, Qasim Pars <qasimpars at gmail.com> wrote:

> Dear users,
>
> I have simulated a protein with simulation time of 200 ns and saving the
> coordinates at every 40 ps. Conformational entropy (~4500 kJ/mol K)
> obtained by Quasiharmonic approach using gmx covar and gmx anaeig tools is
> not consistent with literature (~2500 kJ/mol K). Whereas, the RMSD results
> show that system has reached the convergence.
> Do you think that the problem is the long saving time (every 40 ps) of
> coordinates? Maybe I should redo the simulation with saving the coordinates
> at every 10 ps to capture all conformatinal states of protein during the
> simulation? I am not sure that the saving the coordinates at every 10 ps
> will be enough to get the conformational entropy consisted with literature?
>
> Thanks for any suggestions.
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.