Automated Exploration of Free Energy Landscapes Based on Umbrella Integration
Graduate School of Science, Osaka University, Osaka 565-0871, Japan
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Int. J. Mol. Sci. 2018, 19(4), 937; https://doi.org/10.3390/ijms19040937
Received: 28 February 2018 / Revised: 19 March 2018 / Accepted: 21 March 2018 / Published: 21 March 2018
(This article belongs to the Special Issue Computational Studies of Structure-Dynamics-Function Relationships in Biomolecules)
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.
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MDPI and ACS Style
Mitsuta, Y.; Kawakami, T.; Okumura, M.; Yamanaka, S. Automated Exploration of Free Energy Landscapes Based on Umbrella Integration. Int. J. Mol. Sci. 2018, 19, 937.
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