[gmx-users] Isobaric - isothermal ensemble and Replica Exchange
YLU at zurich.ibm.com
Wed Nov 16 15:10:07 CET 2005
as previously posted in the mailing list, a Replica Exchange Molecular
Dynamics (REMD) simulation has been performed on a protein-ligand-
water system: each replica has been simulated at the same pressure (1
atm) and different temperatures in order to sample temperature space.
Therefore, NPT replicas have been used, and this does NOT of course
represent a random walk distribution, with its probability
distribution having a decreasing exponential trend as pointed in the
paper published on Chemical Physics Letters by Okabe et al in 2001
There is a question that I have now: if in random walk like
distribution an averaged observable is obtainable & computable, what
about the physical significance of parameters that can be obtained
using REMD in isobaric-isothermal ensemble ?
Do you have any suggestions about the data treatment for getting
relevant parameters about the system, e.g., thermodinamic quantities ?
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