[gmx-users] Isobaric - isothermal ensemble and Replica Exchange

Luca Mollica YLU at zurich.ibm.com
Wed Nov 16 15:10:07 CET 2005

Dear all,

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 
(225, 435-439).

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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