Conformationalsampling is one of the most important challenges in simulatingbiologically relevant events in atomistic detail. Temperature replicaexchange molecular dynamics (T-REMD) has been shown successful inspeeding up conformational transitions however for larger and morecomplicated systems the use of T-REMD is still computationallyintensive. Reservoir Replica Exchange Method (R-REMD) can be used toenhance sampling where the conformational search and temperatureequilibration are separated. This allows integrating computationallyefficient search algorithms with replica exchange. The ConformationalSpace Annealing (CSA) method has been shown to be able to determinethe global free energy of proteins efficiently and has successfullybeen used in structure prediction we used it to generate reservoir conformations to be used in R-REMD. Since the initial phase of thesearch was performed via CSA, each temperature rapidly converged totheir equilibrium distributions and significant improvement onconvergence and efficiency was observed on model systems and shortpeptides.

Generating
reservoir conformations for replica exchange through the use of
conformational space annealing method

242nd National Meeting (2011)

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Generating reservoir conformations for replica exchange through the use of conformational space annealing method