Accession Number:

ADA429785

Title:

An Efficient Hybrid Explicit/Implicit Solvent Method for Biomolecular Simulations

Descriptive Note:

Journal article

Corporate Author:

ARMY MEDICAL RESEARCH INST OF INFECTIOUS DISEASES FORT DETRICK MD

Personal Author(s):

• Lee, Michael S.
• Salsbury Jr, Freddie R.
• Olson, Mark A.

Report Date:

2004-07-13

Pagination or Media Count:

13.0

Abstract:

We present a new hybrid explicitimplicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born GB theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid method for evaluating the pairwise electrostatic and GB terms. It is shown that for typical ion and protein simulations our method achieves similar equilibrium and dynamical observables as the conventional particle mesh Ewald PME method. Simulation timings are reported, which indicate that the hybrid method is much faster than PME, primarily due to a significant reduction in the number of explicit water molecules required to model hydration effects.

Descriptors:

• *COST EFFECTIVENESS
• *MACROMOLECULES
• COMPUTERIZED SIMULATION
• REPRINTS
• COMPUTATIONS
• HYBRID SYSTEMS
• ELECTROSTATICS
• MOLECULAR DYNAMICS

Subject Categories:

• Physical Chemistry
• Computer Programming and Software

Distribution Statement:

APPROVED FOR PUBLIC RELEASE