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Automated Exploration of Free Energy Landscapes Based on Umbrella Integration.

ABSTRACT: We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values.

SUBMITTER: Mitsuta Y

PROVIDER: S-EPMC5979611 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Automated Exploration of Free Energy Landscapes Based on Umbrella Integration.

Mitsuta Yuki Y Kawakami Takashi T Okumura Mitsutaka M Yamanaka Shusuke S

International journal of molecular sciences 20180321 4

We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and the transition states were efficiently found in the ascending order of the PMF values. ...[more]

PMID: 29561821

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