PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts

Published: 1 March 2014| Version 1 | DOI: 10.17632/kp87hnf2ky.1
Toni Giorgino


Abstract PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED’s rich syntax to define collective variables (CVs) and VMD’s chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving r... Title of program: PLUMED-GUI (Collective variable analysis plugin) Catalogue Id: AERU_v1_0 Nature of problem Compute and visualize values of collective variables on molecular dynamics trajectories from within VMD, and interactively develop biasing scripts for the estimation of free-energy surfaces in PLUMED. Versions of this program held in the CPC repository in Mendeley Data AERU_v1_0; PLUMED-GUI (Collective variable analysis plugin); 10.1016/j.cpc.2013.11.019 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)



Molecular Biology, Statistical Physics, Biological Sciences, Computational Physics, Thermodynamics