TY - JOUR
T1 - Weighted histogram analysis method for multiple short-time metadynamics simulations
AU - Ono, Junichi
AU - Nakai, Hiromi
N1 - Funding Information:
The authors thank Professor Yasushige Yonezawa at Kindai University for helpful discussions on metaD. This work was supported in part by a Grant-in-Aid for Scientific Research (S) “KAKENHI Grant Number JP18H05264” and a Grant-in-Aid for Specially Promoted Research “KAKENHI Grant Number JP15H05701” from the Japan Society for the Promotion of Science (JSPS). This work was also supported by the Element Strategy Initiative of MEXT, “Grant Number JPMXP0112101003”. The calculations were performed in part at the Research Center for Computational Science (RCCS), Okazaki Research Facilities, National Institutes of Natural Sciences (NIIS), Japan.
Funding Information:
The authors thank Professor Yasushige Yonezawa at Kindai University for helpful discussions on metaD. This work was supported in part by a Grant-in-Aid for Scientific Research (S) “KAKENHI Grant Number JP18H05264 ” and a Grant-in-Aid for Specially Promoted Research “KAKENHI Grant Number JP15H05701 ” from the Japan Society for the Promotion of Science (JSPS). This work was also supported by the Element Strategy Initiative of MEXT , “Grant Number JPMXP0112101003 ”. The calculations were performed in part at the Research Center for Computational Science (RCCS), Okazaki Research Facilities, National Institutes of Natural Sciences (NIIS), Japan.
Publisher Copyright:
© 2020 Elsevier B.V.
PY - 2020/7/16
Y1 - 2020/7/16
N2 - An efficient calculation scheme for obtaining free energy surfaces (FESs) in chemical or biological systems from multiple metadynamics (metaD) simulations was developed. In this study, the biased probability distributions of the collective variables and other degrees of freedom were separately calculated in multiple short-time metaD simulations using the reweighting method. The corresponding equilibrium probability distribution was finally constructed using the weighted histogram analysis method (WHAM). This method was applied for the conformational transitions of alanine dipeptide in the gas phase as an illustrative application. The results confirmed that this method was feasible for efficiently generating the converged FES.
AB - An efficient calculation scheme for obtaining free energy surfaces (FESs) in chemical or biological systems from multiple metadynamics (metaD) simulations was developed. In this study, the biased probability distributions of the collective variables and other degrees of freedom were separately calculated in multiple short-time metaD simulations using the reweighting method. The corresponding equilibrium probability distribution was finally constructed using the weighted histogram analysis method (WHAM). This method was applied for the conformational transitions of alanine dipeptide in the gas phase as an illustrative application. The results confirmed that this method was feasible for efficiently generating the converged FES.
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U2 - 10.1016/j.cplett.2020.137384
DO - 10.1016/j.cplett.2020.137384
M3 - Article
AN - SCOPUS:85084360565
VL - 751
JO - Chemical Physics Letters
JF - Chemical Physics Letters
SN - 0009-2614
M1 - 137384
ER -