Open AccessConstant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
Author(s) -
Brian K. Radak,
Christophe Chipot,
Donghyuk Suh,
Sunhwan Jo,
Wei Jiang,
J. C. Phillips,
Klaus Schulten,
Benoît Roux
Publication year - 2017
Publication title -
journal of chemical theory and computation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.001
H-Index - 185
eISSN - 1549-9626
pISSN - 1549-9618
DOI - 10.1021/acs.jctc.7b00875
Subject(s) - molecular dynamics , computer science , scalability , constant (computer programming) , monte carlo method , computational science , force field (fiction) , canonical ensemble , supercomputer , on the fly , field (mathematics) , statistical physics , chemistry , computational chemistry , physics , parallel computing , artificial intelligence , mathematics , statistics , database , pure mathematics , programming language , operating system
An increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementation of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.