Literature DB >> 28147529

Enhancement of canonical sampling by virtual-state transitions.

Junichi Higo1, Kota Kasahara2, Bhaskar Dasgupta1, Haruki Nakamura1.   

Abstract

A novel method was developed to enhance canonical sampling. A system is divided into virtually introduced sub-states, called "virtual states," which does not exist in reality. The configuration sampling is achieved by a standard canonical sampling method, the Metropolis Monte Carlo method, and confined in a virtual state for a while. In contrast, inter-virtual state motions are controlled by transition probabilities, which can be set arbitrarily. A simple recursive equation was introduced to determine the inter-virtual state transition probabilities, by which the sampling is enhanced considerably. We named this method "virtual-system coupled canonical Monte Carlo (VcMC) sampling." A simple method was proposed to reconstruct a canonical distribution function at a certain temperature from the resultant VcMC sampling data. Two systems, a one-dimensional double-well potential and a three-dimensional ligand-receptor binding/unbinding model, were examined. VcMC produced an accurate canonical distribution much more quickly than a conventional canonical Monte Carlo simulation does.

Entities:  

Year:  2017        PMID: 28147529     DOI: 10.1063/1.4974087

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  2 in total

1.  GA-guided mD-VcMD: A genetic-algorithm-guided method for multi-dimensional virtual-system coupled molecular dynamics.

Authors:  Junichi Higo; Ayumi Kusaka; Kota Kasahara; Narutoshi Kamiya; Itaya Hayato; Xie Qilin; Takuya Takahashi; Ikuo Fukuda; Kentaro Mori; Yutaka Hata; Yoshifumi Fukunishi
Journal:  Biophys Physicobiol       Date:  2020-12-26

2.  Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism.

Authors:  Junichi Higo; Kota Kasahara; Mitsuhito Wada; Bhaskar Dasgupta; Narutoshi Kamiya; Tomonori Hayami; Ikuo Fukuda; Yoshifumi Fukunishi; Haruki Nakamura
Journal:  Protein Eng Des Sel       Date:  2019-12-31       Impact factor: 1.650

  2 in total

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