From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Fri Oct 19 2012 - 09:36:38 CDT
I am going to start running some replica exchange simulations and was wondering if there were any namd options that are incompatible with this type of simulation? Right now I'm running the simulation with AMBER forcefield in a truncated octahedron of solvent. Going through the scripts that are distributed with namd, I don't see any reason why this wouldn't work but the documentation does somewhat imply that the simulation needs to be run in the manner presented in the example.
If anyone has any experience with this type of simulation, I'd appreciate any input. Also, if there are any specific incompatibilities not listed in the brief documentation I'd love to know.
Thanks a lot,
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