Web Release Date: December 4,
Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces
Laboratory of Biophysics, Center for Biologics Evaluation and Research, FDA, 1401 Rockville Pike, Rockville, Maryland 20852-1448
Laboratory of Structural Biology, Division of Computer Research & Technology, National Institutes of Health, Bethesda, Maryland 20892
Received: April 17, 2003
In Final Form: October 3, 2003
Abstract:
A straightforward method that accounts for the long-range Lennard-Jones (LJ) terms in constant pressure molecular dynamics simulations is presented. This long-range correction (LRC) consists of an additional applied pressure tensor which is periodically calculated from the difference of instantaneous pressures at the selected cutoff and a very long cutoff. It provides results that are nearly independent of the LJ cutoff distance at negligible additional calculation costs, and is particularly suited for anisotropic systems such as liquid/liquid interfaces or heterogeneous macromolecules where approximations based on spherically symmetric radial distribution functions are expected to fail. The utility of the method is demonstrated for a series of alkanes and water, and for interfaces including a lipid bilayer. The LRC increases densities and decreases isothermal compressibilities, with the changes larger for alkanes than for water (where the long-range interactions are dominated by electrostatic interactions). While implementation of the LRC will not necessarily improve agreement with a particular experiment, it will provide a baseline for improvements in a parameter set that are consistent with the long-range Lennard-Jones interactions.
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