Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aeru_v1_0.tar.gz(31 Kbytes)|
|Manuscript Title: PLUMED-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts|
|Authors: Toni Giorgino|
|Program title: PLUMED-GUI (Collective variable analysis plugin)|
|Catalogue identifier: AERU_v1_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 185(2014)1109|
|Programming language: TCL/TK.|
|Computer: Workstations, PCs.|
|Operating system: Linux/Unix, OSX, Windows.|
|RAM: Sufficient to run PLUMED  and VMD .|
|Keywords: Graphical User Interface, VMD, PLUMED, Molecular Dynamics, Collective Variables, Metadynamics.|
|Classification: 3, 23.|
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.
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.
Tested on systems up to 100,000 atoms.
VMD-PLUMED is not a standalone program but a plugin that provides access to PLUMED's analysis features from within VMD.
Distributed with VMD since version 1.9.0. Manual update may be required to access the latest features.
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.
|||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) 33-38.|
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