Replica Exchange with Solute Tempering: A Method for Sampling Biological Systems in Explicit Water

An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2005-09, Vol.102 (39), p.13749-13754
Main Authors: Liu, Pu, Kim, Byungchan, Friesner, Richard A., Berne, B. J.
Format: Article
Language:English
Subjects:
Algorithms
Arithmetic mean
Degrees of freedom
Dipeptides - chemistry
Ergodic measures
High temperature
Models, Chemical
Molecules
Monte Carlo Method
Monte Carlo simulation
Physical Sciences
Potential energy
Protein Conformation
Protein folding
Proteins - chemistry
Sampling
Solutes
Solution chemistry
Solutions - chemistry
Solvents
Tempering
Trajectories
Water
Water - chemistry
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Summary:An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST is compared with standard replica exchange for an alanine dipeptide molecule in water. The comparisons confirm that REST greatly reduces the number of CPUs required by regular replica exchange and increases the sampling efficiency. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0506346102