Paper Citing NAMD - Abstract
Sakuraba, Shun; Matubayasi, Nobuyuki
ERmod: Fast and Versatile Computation Software for Solvation Free Energy with Approximate Theory of Solutions
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1592-1608, AUG 5 2014
ERmod is a software package to efficiently and approximately compute the solvation free energy using the method of energy representation. Molecular simulation is to be conducted at two condensed-phase systems of the solution of interest and the reference solvent with test-particle insertion of the solute. The subprogram ermod in ERmod then provides a set of energy distribution functions from the simulation trajectories, and another subprogram slvfe determines the solvation free energy from the distribution functions through an approximate functional. This article describes the design and implementation of ERmod, and illustrates its performance in solvent water for two organic solutes and two protein solutes. Actually, the free-energy computation with ERmod is not restricted to the solvation in homogeneous medium such as fluid and polymer and can treat the binding into weakly ordered system with nano-inhomogeneity such as micelle and lipid membrane. ERmod is available on web at http://sourceforge.net/projects/ermod. (C) 2014 Wiley Periodicals, Inc.
