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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 [1] and VMD [2].
Keywords: Graphical User Interface, VMD, PLUMED, Molecular Dynamics, Collective Variables, Metadynamics.
Classification: 3, 23.

Subprograms used:
Cat Id Title Reference
AEEE_v2_0 PLUMED CPC 185(2014)604

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.

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:
VMD-PLUMED is not a standalone program but a plugin that provides access to PLUMED's 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:
[1] 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.
[2] W. Humphrey, A. Dalke, K. Schulten, VMD: visual molecular dynamics, J Mol Graph 14 (1996) 33-38.