TCB Seminar

“Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems with NAMD”

Ph.D. Brian Radak
Argonne Leadership Computing Facility
Argonne, IL

Wednesday, July 19, 2017
12:00 am
3269 Beckman Institute

Abstract

Constant-pH molecular dynamics (MD) is an increasingly popular approach for accounting for multiple protonation states during biomolecular simulations. Nonetheless, although many such approaches have been proposed they have not been widely adopted, perhaps because each has drawbacks for different kinds of applications and/or size scales.This work describes the efficient implementation and improvement of a recent proposal for constant-pH MD based on a hybrid nonequilibrium MD/Monte Carlo technique which is now combined with the highly portable and scalable NAMD simulation engine. The method has a number of appealing features: 1) it rigorously and directly samples the correct semi-grand canonical ensemble, 2) it is applicable in both aqueous and crowded environments (e.g. lipid membranes), 3) its cost does not increase with respect to the number of titration sites, 4) it places no constraints on the form of the force field, and 5) the efficiency and performance can be straightforwardly improved on-the-fly for any given system. The implementation is appropriate for many biomolecular applications but the examples here are designed to emphasize medium and large scale applications on next-generation supercomputing architectures.