Development and Application of a Method for Including pH Effects in Large Scale Molecular Dynamics Simulations

Event Sponsor: 
Argonne Leadership Computing Facility Seminar
Start Date: 
Oct 16 2015 - 10:30am
Building 240/Room 4301
Argonne National Laboratory
Brian K. Radak
Speaker(s) Title: 
University of Chicago
Tim Williams

Standard molecular simulation methods based on classical force fields typically assume only a fixed protonation state of systems. This assumption generally only permits a limited treatment of pH effects, for example, consideration of extreme acidic/basic conditions or situations where a small number of protonation states can be explicitly enumerated. Importantly, the standard approach cannot be scaled to chemical systems with a large number of titrateable sites such as lipid head groups or assemblies of protein subunits. This talk will describe the development of a scalable and extensible method for including pH effects in molecular dynamics simulations. In contrast to other constant pH methods, the new method, based on a hybrid of non-equilibrium molecular dynamics and Monte Carlo, can be easily scaled to handle large heterogeneous systems, i.e., not only globular proteins. The applicability of the method will be discussed and motivated by previous studies in computational enzymology as well as ongoing work with membranes and membrane proteins.

Miscellaneous Information: 

Conference room is located on the fourth floor. Go to the right after you get off of the elevator. The room will be on the left side.

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