Paper Citing NAMD - Abstract
Hixson, Christopher Adam; Wheeler, Ralph A.
Pressure Annealing as a Complement to Temperature Annealing To Find Low-Energy Structures of Oligomeric Molecules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1883-1894, JUL 2009
Finding the lowest-energy geometry of a molecule or collection of molecules is a fundamental challenge of modern computational chemistry and is closely related to the more general problem of optimizing a function. Temperature annealing, popularly called simulated annealing, is a powerful and commonly used technique, but it is not well suited to conformational sampling of long, oligomeric molecules. A method is presented herein that incorporates pressure as an optimization parameter to complement temperature annealing, and several tests of its effectiveness are described. Bayesian statistical analysis shows that pressure-temperature annealing confers no advantage in control simulations of Lennard-Jones particles, but it yields lower-energy structures than pure temperature annealing with significant credibility for two model polyethers, monoglyme (CH(3)OCH(2)CH(2)OCH(3)) and tetraglyme [CH(3)(OCH(2)CH(2))(4)OCH(3)].
