Paper Citing NAMD - Abstract
Lettieri, Steven; Zuckerman, Daniel M.
Accelerating molecular monte carlo simulations using distance and orientation-dependent energy tables: Tuning from atomistic accuracy to smoothed "coarse-grained" models
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:268-275, JAN 30 2012
Typically, the most time consuming part of any atomistic molecular simulation is the repeated calculation of distances, energies, and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed-up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (precalculation) of distance- and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomisticbut rigidbenzene molecules at standard temperature and density. In particular, using ${\cal O}$(1) GB of RAM, we construct an energy look-up table, which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 2450 as compared to an ordinary (exact) Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications, greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules. (C) 2011 Wiley Periodicals, Inc. J Comput Chem, 2012
