PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts ?
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 PLUMEDs rich syntax to define collective variables (CVs) and VMDs 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 reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Script development takes place without leaving VMD, thus enabling an incremental tryseemodify development model for molecular metrics. Program title: PLUMED-GUI (Collective variable analysis plugin) Catalogue identifier: AERU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERU_v1_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: 3-clause BSD Open Source No. of lines in distributed program, including test data, etc.: 2651 No. of bytes in distributed program, including test data, etc.: 32359 Distribution format: tar.gz Programming language: TCL/TK. Computer: Workstations, PCs. Operating system: Linux/Unix, OSX, Windows. RAM: Sufficient to run PLUMED [1] and VMD [2]. Classification: 3, 23. Subprograms used: 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. Solution method: A graphical user interface is integrated in VMD and allows the user to interactively develop and run analysis scripts. Menus and dialogs provide mnemonics and documentation on the syntax to define complex CVs. Restrictions: Tested on systems up to 100,000 atoms. Unusual features: VMDPLUMED is not a standalone program but a plugin that provides access to PLUMEDs analysis features from within VMD. Additional comments: Distributed with VMD since version 1.9.0. Manual update may be required to access the latest features. Running time: Computations of the values of collective variables, performed by the underlying PLUMED code, depends on the size of the system and the length of the trajectory; it is generally negligible with respect to simulation time. References: G. A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED 2: New feathers for an old bird, Computer Physics Communications 185 (2014) 604. W. Humphrey, A. Dalke, K. Schulten, VMD: visual molecular dynamics, J Mol Graph 14 (1996) 3338.
plumed molecular dynamics vmd collective variables graphical user interface metadynamics