Robert Latour
Clemson University
latourr at

New LAMMPS Modules for the Simulation of Protein-Surface Interactions with CHARMM

The simulation of protein-surface interactions represents several challenges that are unique to this type of molecular system. In particular, the molecular environment at the interface can be expected to be distinctly different from either the solution or solid phases themselves, thus requiring its own separate set of force field parameters to independently control interfacial behavior. Secondly, the extreme complexity of the behavior of proteins at interfaces requires the use of advanced sampling methods that can be used to generate a Boltzmann-weighted ensemble of states within a reasonable timeframe. Thirdly, the CHARMM protein force field requires the use of CMAP cross-terms to properly represent protein folding behavior. We are developing new LAMMPS modules to meet each of these needs: (1) A new set of pair_style modules to implement an interfacial force field with its own independent set of vdW and partial charge parameters, (2) a module to implement a new advanced sampling replica-exchange method for large molecular systems called TIGER2A, and (3) a new module to include CMAP cross-terms for the CHARMM protein force field. This poster will provide an overview of the features and use of each of these new capabilities for LAMMPS.