Paper Citing NAMD - Abstract
Schneider, Olaf; Sternberg, Ulrich; Vondrous, Alexander
PARALLEL MOLECULAR DYNAMICS SIMULATION USING A HYBRID FORCE FIELD WITH QUANTUM CHEMICAL CHARGE CALCULATIONS
CLUSTER COMPUTING AND MULTI-HOP NETWORK RESEARCH, 73-90, 2010
The simulation of biomolecules like proteins in their natural environment is computational demanding and parallelization is a must to simulate relevant time scales within a reasonable computation time. The software COSMOS uses a mixed approach of classical molecular dynamics (MD) and quantum chemistry (QC) by incorporating atomic charge computed using the Bond Polarization Theory (BPT) into the force field. To parallelize the MD we used an atom-decomposition approach with replicated data. A kind of greedy algorithm yields a partition of the atoms without dividing chemical bonds. The parallel version of the force field COSMOS-NMR is implemented using MPI. We present the results of performance measurements. As test case we used an ice crystal heated over a picosecond. The computations are performed on a HPC cluster with InfiniBand. It turns out, that our code greatly benefits from the low latency of the interconnect.
