MOLECULAR VISUALIZATION PROGRAM VMD

$68,666P41FY2001RRNIH

University Of Illinois Urbana-Champaign, Champaign IL

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Abstract

Current emphasis is on integration methods for molecular dynamics that can be incorporated into NAMD. The relatively high cost of fast full electrostatics is reduced in NAMD by a factor of four through the use of Verlet-I/r-RESPA/impulse multiple time stepping, in which the full electrostatics is evaluated only every 4 fs. To further increase the time step for these calculations, the mollified impulse method [60] was devised and implemented for flexible water. The variants of the method tested thus far enable an increase in the longest time step from 4 fs to 6.25 fs without introducing Langevin damping. The cause of the time step barrier at 7 fs is under investigation and possible remedies are being devised. Also begun is work on an optimal choice of the force partitioning for multiple time stepping. Observations suggest that non-linear instabilities limit the time step. A related project is making advances in understanding this phenomenon.

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