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

[Qasim Pars]

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.