A simplified confinement method for calculating absolute free energies and free energy and entropy differences.

ABSTRACT: A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the α-helix ↔ β-sheet transition in a 16-residue peptide modeled in

SUBMITTER: Ovchinnikov V 

PROVIDER: S-EPMC3569517 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature