Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations.

ABSTRACT: Molecular dynamics-based free energy calculations allow the determination of a variety of thermodynamic quantities from computer simulations of small molecules. Thermodynamic integration (TI) calculations can suffer from instabilities during the creation or annihilation of particles. This "singularity" problem can be addressed with "soft-core" potential functions which keep pairwise interaction energies finite for all configurations and provide smooth free energy curves. "One-step" transformations, in which electrostatic and van der Waals forces are simultaneously modified, can be simpler and less expensive than "two-step" transformations in which these properties are changed in separate calculations. Here, we study solvation free energies for molecules of different hydrophobicity using bo

SUBMITTER: Steinbrecher T 

PROVIDER: S-EPMC3187911 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature