An optimized replica exchange molecular dynamics method - PubMed (original) (raw)
. 2009 Feb 21;130(7):074906.
doi: 10.1063/1.3077857.
Affiliations
- PMID: 19239315
- DOI: 10.1063/1.3077857
An optimized replica exchange molecular dynamics method
Hiqmet Kamberaj et al. J Chem Phys. 2009.
Abstract
We introduce a new way to perform swaps between replicas in replica exchange molecular dynamics simulations. The method is based on a generalized canonical probability distribution function and flattens the potential of mean force along the temperature coordinate, such that a random walk in temperature space is achieved. Application to a Go model of protein A showed that the method is more efficient than conventional replica exchange. The method results in a constant probability distribution of the replicas over the thermostats, yields a minimum round-trip time between extremum temperatures, and leads to faster ergodic convergence.
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