Hi Agnivo; Yes, the idea of freezing the solvent or the protein in many times is to sample the "non-equilibrium thermal process". It will remain in the target temperature on average, over many fixed configurations obtained by different NVT runs (equilibrium runs). But you may need to run this many K times to get a good statistic as I said. Concerning NVE, yes, do the same fixing approach with the protein. But as I mentioned earlier, this is quite heuristic approach, I suggest you to talk with any faculty member having background in non-equilibrium processes if this approach mimics what you need.
Best, -m -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
