Seminars & Events

Argonne Leadership Computing Facility
"Methodological Developments for Molecular Dynamics Simulations on Massively Distributed Computing Platforms"

DATE: August 9, 2011
TIME: 1:30 PM - 2:30 PM
SPEAKER: Wei Jiang, Computational Postdoctoral Fellow
LOCATION: Building 240 / Conference Room 4301, Argonne National Laboratory
HOST: Katherine Riley

Description:
Progresses in two computational projects, computation of absolute binding free energy and implementation/application of Drude polarizable force field in NAMD will be reported. The heart of computation strategy for ligand binding free energy is a novel Distributed Replica (parallel/parallel) mode, which resolves the ‘embarrassingly parallel’ problems in free energy computation. Parallel performance on Blue Gene/P and CRAY XT5 with parallel/parallel mode will be shown. This strategy also facilitates a replica exchange scheme by point-to-point communications, forming a distributed Hamiltonian exchange molecular dynamics method. The novel methodology will be demonstrated with 3 difficult cases of ligand binding calculations, although the overall methodology is applicable to many other quantitative biological simulations. For the Drude oscillator model, the implementation strategy follows the seminal hybrid force/domain decomposition of NAMD and therefore realizes unprecedented large-scale molecular dynamics simulations with all-atom polarizable force field. Implementation details will be provided and parallel performance of general Drude model on Blue Gene/P will be shown. Application of NAMD of Drude model will be demonstrated with a novel large-scale simulation of salt solution at physiological concentration.

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