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

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 wrote: > > Hi Qasim, > > The RMSD is not good for assessing convergence, especially if it goes above > 0.5

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

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 wrote: > Dear users, > > I have simulated a protein with simulation time of 200 ns and saving the > coordinates at

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

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