Dear Justin, No dear I have not modelled the membrane, my protein is a simple protein which contained a loop about 59 amino acids. So I am intrested to model this loop through MD simulation. In this concerned I did 15 ns simulations, but right now don't know how to perform sampling for my protein (which is not a membrane, thermophilic or mesophilic protein) on same temperature i.e. 300k. In this regard is it correct to perform REMD, if yes then tell me how to perform it on single CPU? I am asking from you again to sure I can perform ot is it right to use REMD in my protein condition which in not a thermophilic protein. I think that REMD can only apply to those proteins which are thermophilic or mesophilic. please comment on this.
Yes I wanted to sample loop dynamics, for which you have mentioned to run several simulations at the relevant (physiological?) temperature. Is it mean to run several (2,3,4..etc) diferent simulations at different time steps like 10ns, 15ns, 20ns, 30 ns etc. and analyze those results to obtain some averages from each and every simulations but it gives several averages values then how to sample all these simulations and finally how to get the average from these simulations. -- Pawan
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