Paper Citing NAMD - Abstract
Huggins, David J.
Benchmarking the thermodynamic analysis of water molecules around a model beta sheet
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1383-1392, JUN 5 2012
Water molecules play a vital role in biological and engineered systems by controlling intermolecular interactions in the aqueous phase. Inhomogeneous fluid solvation theory provides a method to quantify solvent thermodynamics from molecular dynamics or Monte Carlo simulations and provides an insight into intermolecular interactions. In this study, simulations of TIP4P-2005 and TIP5P-Ewald water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. This allows the method to be benchmarked and provides information about the effect of a protein on the thermodynamics of nearby water molecules. The results show that the enthalpy converges with relatively little sampling, but the entropy and thus the free energy require considerably more sampling to converge. The two water models yield a very similar pattern of hydration sites, and these hydration sites have very similar thermodynamic properties, despite notable differences in their orientational preferences. The results also predict that a protein surface affects the free energy of water molecules to a distance of approximately 4.0 angstrom, which is in line with previous work. In addition, all hydration sites have a favorable free energy with respect to bulk water, but only when the waterwater entropy term is included. A new technique for calculating this term is presented and its use is expected to be very important in accurately calculating solvent thermodynamics for quantitative application. (c) 2012 Wiley Periodicals, Inc.
