[gmx-users] Using thermostats to create temperature gradient in system

[Suzen, Mehmet]

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