Paper Citing NAMD - Abstract
Liu, Peng; Dehez, Francois; Cai, Wensheng; Chipot, Christophe
A Toolkit for the Analysis of Free-Energy Perturbation Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2606-2616, AUG 2012
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.
