TCB Publications - Abstract

Brian K Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C Phillips, Klaus Schulten, and Benoît Roux. Constant-pH molecular dynamics simulations for large biomolecular systems. Journal of Chemical Theory and Computation, 13:5933-5944, 2017. (PMC: PMC5726918)

RADA2017 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.

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