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

[Qasim Pars]

Hi Tsjerk,

Yes, you are right but I was also wondering the comments/suggestions on conformational entropy calculation. 



> On 8 Jun 2016, at 23:33, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> 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.
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