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Parallel Generalized Born Implicit Solvent Calculations with NAMD
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DOI：10.1021/ct200563j.png)
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摘要
En 中文
Accurate electrostatic descriptions of aqueous solvent are critical for simulation studies of biomolecules, 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 heterogeneous distribution of atoms, and the necessary 3-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 similar to 250 000 atoms.
Keyword:
MOLECULAR-DYNAMICS SIMULATIONS
AMBER FORCE-FIELD
NUCLEIC-ACIDS
CONTINUUM ELECTROSTATICS
BIOMOLECULAR SYSTEMS
SINGLE RIBOSOMES
STRUCTURAL BASIS
MESSENGER-RNA
FREE-ENERGIES
L1 STALK
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期刊
IF:
5.5
论文数:
1.1W
被引数:
5.4W
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引用论文
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