SC13 Denver, CO

The International Conference for High Performance Computing, Networking, Storage and Analysis

A Scalable Hamiltonian Hybrid DFT/PMM-MD Approach for Accurately Simulating Biomolecules on SuperMUC.


Authors: Magnus Schwörer (Ludwig-Maximilians Universität München), Paul Tavan (Ludwig-Maximilians Universität München), Ferdinand Jamitzky (Leibniz Supercomputing Center), Helmut Satzger (Leibniz Supercomputing Center), Gerald Mathias (Ludwig-Maximilians Universität München)

Abstract: In this poster, we present an Hamiltonian approach for hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment. It guarantees energy conservation and treats the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion using hierarchically nested fast multipole expansions. Our implementation links the MPI/OpenMP-parallel PMM-MD code IPHIGENIE (developed by us under GPL) to the well-established DFT code CPMD and offers a unique tool which greatly enhances the accuracy of the description of the condensed phase environment of a DFT molecule compared to conventional unpolarizable MM force fields. It scales very well even for small simulation systems and makes studies of large DFT molecules solvated in accurately modeled condensed phase feasible.

Poster: pdf
Two-page extended abstract: pdf


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