title: A Toolkit for the Analysis of Free-Energy Perturbation Calculations.
abstract: As computational power inexorably continues to grow, harnessing the capabilities of novel processing units and architectures, free-energy calculations are progressively brought to the level of routine modeling tools for exploring the thermodynamic properties of increasingly larger molecular assemblies. Within these premises, free-energy perturbation (FEP) arguably represents the most commonly chosen approach for tackling transformations of a chemical nature between thermodynamic states. To augment the accuracy, the precision, and, hence, the reliability of these calculations, a number of good practices have been established. In the present contribution, a new toolkit, coined ParseFEP, is proposed to follow these prescriptions in a user-friendly environment. Written as a Tcl plugin, it allows FEP calculations carried out using the popular molecular-dynamics package NAMD to be analyzed seamlessly within the visualization platform VMD. The potential of the toolkit is probed through a number of illustrative examples, which demonstrate cogently how pathological cases, often related to convergence issues, can be detected and remedied by means of a pictorial approach.
authors.affiliation: College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Liu
authors.affiliation: Équipe de dynamique des assemblages membranaires, UMR 7565, Nancy Université, BP 239, 54506 Vandoeuvre-lès-nancy cedex, France.
authors.forename: François
authors.initials: F
authors.lastname: Dehez
authors.affiliation: College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Cai
authors.affiliation: Équipe de dynamique des assemblages membranaires, UMR 7565, Nancy Université, BP 239, 54506 Vandoeuvre-lès-nancy cedex, France.|Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801, United States.
authors.forename: Christophe
authors.initials: C
authors.lastname: Chipot