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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