Hi Tsjerk, thanks actually my protein is quite larg (509 aa).i had divided my trajectory in different part and according to your suggestion i calculated cosine-content for all, and find that trajectory from 5to15 ns and 18to25ns having cosine value very less about 0.03 in both cases(with and without ligands), while other combination showing higher values (>0.6).so i think my system is Ist converges around 5ns and maintaining it up to 15 ns after that it may be few conformational fluctuation occurring and finally it get stabilized from 18to15ns.may that part 15to18ns trajectory is transition period between to conformational fluctuation. i have also calculated temp. and pressure during whole simulation and i find that it is exact Gaussian between 5to25ns.so my confusion is whether i take my trajectory for ED analysis is from 5to15 or 18to25 or whole from 5to25, but 5to25 showing value of cosine >0.6.
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