Dataset Information

MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.

ABSTRACT: Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Unfortunately, testing these methods remains expensive. We propose a Molecular Dynamics Meta-Simulator (MDMS) based on transition state theory to simulate a replica exchange simulation, eliminating the need to run explicit dynamics between exchange attempts. MDMS simulations allow for rapid testing of new replica exchange based methods, greatly reducing the amount of time needed for new method development.

SUBMITTER: Smith DB

PROVIDER: S-EPMC3472454 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

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MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.

Smith Daniel B DB Okur Asim A Brooks Bernard B

Chemical physics letters 20120719

Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Unfortunately, testing these methods remains expensive. We propose a Molecular Dynamics Meta-Simulator (MDMS) based on transition state theory to simulate a replica exchange ...[more]

PMID: 23087450

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Dataset Information

MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.

Publications

MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.

Similar Datasets

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