**Accelerating molecular monte carlo simulations using distance and
orientation-dependent energy tables: Tuning from atomistic accuracy to
smoothed "coarse-grained" models**

S Lettieri and DM Zuckerman, JOURNAL OF COMPUTATIONAL CHEMISTRY, 33, 268-275 (2012).

DOI: 10.1002/jcc.21970

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

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