Hello:
I've finished a replica exchange simulation with 72 replica
(300K-580K) under explicit solvent model. It generate 72 trajectory and
the replica since to "cross" well with neighboring temperature. Here is
the figure:
http://dl.dropbox.com/u/56271062/REMD.png
I am just wondering how can we generate and visualize the system at
300 K with that at 400-500 K? There is a ligand in my system, and it is
expected to escape binding pocket with large loop movement....
thank you very much
best
Albert
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