Premium
Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems
Author(s) -
Sakae Yoshitake,
Straub John E.,
Okamoto Yuko
Publication year - 2019
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25735
Subject(s) - crossover , molecular dynamics , dihedral angle , monte carlo method , genetic algorithm , algorithm , sampling (signal processing) , computer science , statistical physics , chemistry , computational chemistry , molecule , mathematics , physics , artificial intelligence , statistics , machine learning , hydrogen bond , organic chemistry , filter (signal processing) , computer vision
We propose a molecular simulation method using genetic algorithm (GA) for biomolecular systems to obtain ensemble averages efficiently. In this method, we incorporate the genetic crossover, which is one of the operations of GA, to any simulation method such as conventional molecular dynamics (MD), Monte Carlo, and other simulation methods. The genetic crossover proposes candidate conformations by exchanging parts of conformations of a target molecule between a pair of conformations during the simulation. If the candidate conformations are accepted, the simulation resumes from the accepted ones. While conventional simulations are based on local update of conformations, the genetic crossover introduces global update of conformations. As an example of the present approach, we incorporated genetic crossover to MD simulations. We tested the validity of the method by calculating ensemble averages and the sampling efficiency by using two kinds of peptides, ALA3 and (AAQAA) 3 . The results show that for ALA3 system, the distribution probabilities of backbone dihedral angles are in good agreement with those of the conventional MD and replica‐exchange MD simulations. In the case of (AAQAA) 3 system, our method showed lower structural correlation of α ‐helix structures than the other two methods and more flexibility in the backbone ψ angles than the conventional MD simulation. These results suggest that our method gives more efficient conformational sampling than conventional simulation methods based on local update of conformations. © 2018 Wiley Periodicals, Inc.