David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten.
Parallel generalized Born implicit solvent calculations with
NAMD.
Journal of Chemical Theory and Computation, 7:3635-3642, 2011.
(PMC: 3222955)
TANN2011A
Accurate electrostatic descriptions of aqueous solvent are critical for simulation studies of
bio-molecules, but the computational cost of explicit treatment of solvent is very high. A
computationally more feasible alternative is a generalized Born implicit solvent description
which models polar solvent as a dielectric continuum. Unfortunately, the attainable
simulation speedup does not transfer to the massive parallel computers often employed
for
simulation of large structures. Longer cutoff distances, spatially heterogenous distribution
of atoms and the necessary three-fold iteration over atom-pairs in each timestep combine
to challenge efficient parallel performance of generalized Born implicit solvent algorithms.
Here we report how NAMD, a parallel molecular dynamics program, meets the challenge
through a unique parallelization strategy. NAMD now permits efficient simulation of large
systems whose slow conformational motions benefit most from implicit solvent
descriptions due to the inherent low viscosity. NAMD's implicit solvent performance is
benchmarked and then illustrated in simulating the ratcheting Escherichia coli
ribosome involving 250,000 atoms.
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250,000 atoms.
