Dr. Brian Radack
Biochemistry and Molecular Biology
University of Chicago
Chicago, Illinois

Friday, July 24, 2015
3:00 pm (CT)
3269 Beckman Institute

Abstract

pH is an essential environmental parameter for biological systems, yet most simulation protocols only consider it in an ad hoc fashion. As such, the past decades have seen a proliferation of methods for simulations at constant pH, but each tends to have distinct limitations, especially in terms of the scaling cost as the number of titrateable sites increases. Here I will describe recent efforts to implement and parameterize a constant pH method in NAMD, as well as refine its efficiency such that it is appropriate for large biological systems in explicit solvent.