Showing papers by "Glenn J. Martyna published in 1998"

Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems

Abstract: In this paper, we deal with the handling of the electrostatic forces in complex molecular systems. In particular, we focus on instabilities experienced by reversible multiple time step algorithms when used in conjunction with Ewald summation techniques for periodic systems. We show that energy conservation is negatively affected by the intra-molecular energy term due to electrostatic excluded contacts required by the most frequently used of the modern force fields for biomolecular systems. These effects are due to a non-complete cancellation of the intra-molecular electrostatic energy and forces at intermediate or long time steps.

Molecular dynamics studies of the hexagonal mesophase of sodium dodecylsulphate in aqueous solution

Abstract: Molecular dynamics calculations using a recently proposed simulation methodology (Martyna, G. J., Tuckerman, M. E., Tobias, D. J., and Klein, M. L., 1996, Molec. Phys., 87, 1117) have been carried out to investigate the structural properties of the sodium dodecylsulphate (SDS)-water system in the lyotropic liquid crystalline mesophase E. The simulation system consisted of two cylindrical aggregates, each containing 128 dodecylsulphate anions, plus 256 sodium counterions and 4350 water molecules. The system had periodic boundary conditions and initially overall hexagonal symmetry. A 260ps trajectory was then generated at constant temperature (T = 333 K) and constant pressure (P = 0) using a new molecular dynamics package (PINY-MD), which utilizes a timestep almost an order of magnitude larger than the usual value. The structural and dynamic results are compared with previous simulations reported for quasi-spherical SDS micelles and experimental data on the same system. In agreement with experiment, the sim...