A Plumed collective variable analysis tool for VMD (Plumed-GUI, v 2.0)
To use this plugin, you will need PLUMED's driver and/or plumed executables. Download it from the installation section below.
The PLUMED-GUI collective variable analysis tool is a plugin for the Visual Molecular Dynamics (VMD) software that provides access to the extensive set of collective variables (CV) defined in the PLUMED software. It allows you to:
- analyze the currently loaded trajectory by evaluating and plotting arbitrary CVs
- use VMD's atom selection keywords to define atom groups and ready-made templates for common CVs
- export the CV definition file for use in MD simulations
- prepare reference files for RMSD, path-variable, native contacts, etc.
- analyze DCD files in batches
Both Plumed 2.0 and Plumed 1.3 are supported.
VMD versions 1.9.0 is distributed with PLUMED GUI v0.9. To upgrade, download the plugin and follow the installation instructions in the archive.
The usage of the plugin is straightforward.
From VMD's main window, select "Extensions > Analysis > Collective variable analysis (PLUMED)"
- Edit the CV definition file, defining one or more CVs
- Enter the number of CVs defined in the corresponding box (this will be fixed in a future PLUMED release)
- Click "Plot". This will open a plot window with the selected CVs.
Square brackets can be used to conveniently define atom groups (Ctrl-G). During evaluation, atom selection keywords in square brackets are replaced with a list of the corresponding serial numbers for the top molecule.
When Plot is clicked, the currently loaded trajectory is exported to a temporary directory (shown in the console), and the driver utility is invoked. If there are no errors, a plot will show the CVs evaluated on the frames of the current trajectory.
Troubleshooting: In case of errors, the console will provide diagnostics and the location of the temporary directory where computations are run. Common sources of error are:
- Hills deposition should be disabled.
- Improperly set periodic boundary conditions, especially when dealing with non-wrapped solvent or with MD engines which "break" molecules by wrapping them.
The File menu
CV definition files can be opened, edited and saved as usual. Save and Save as... save the currently open file verbatim, while the Export... function performs the atom selection replacements (see below), thus creating a META_INP file that can be used directly in simulations.
The Edit menu
The Edit menu provides the usual cut-copy-paste text-editing options.
The Templates menu
Elements in the Templates menu provides shortcuts for most CVs supported by PLUMED. Please refer to PLUMED's user's guide for the full syntax.
The Electrostatic energy and Dipole CVs require charges to be defined in the currently loaded molecule, so AMBER or CHARMM topology file have to be loaded beforehand.
Structure files (used for RMSD, Z_PATH, S_PATH, etc.) must be referenced by absolute pathname.
The template menu does not hold the full list of the CVs implemented in PLUMED, but all of them will work anyway when typed in.
The Structure menu
The Structure menu provides functions for entering complex CVs.
Reference structures for RMSD and path variables
The Structure>Prepare reference structure... dialog can be used to prepare pseudo-PDB files that can be used as reference structures for RMSD, path-variables, etc. Two VMD atom selections are required to define the set of atoms that will be used for alignment (alignment set) and for the distance measurement (displacement set), respectively. The currently selected frame of the top molecule is used to create a reference file; numbering can be altered to conform to another molecule. The file format is specified in the 'Path collective variables' section of the PLUMED manual.
- After generating the structures, remember to set the top molecule to the one you want to analyze.
Structures must be referenced by absolute pathname in the PLUMED script.
- The RMSD keyword has been renamed to MSD in PLUMED 1.3.
The Structure>Native contacts CV inserts a native-contacts CV. The currently selected frame of the top molecule is taken as the native state. Atom numbers are adapted to fit the structure indicated in the target molecule field. If selection 2 is given, only intermolecular contacts (between selection 1 and 2) are counted. Otherwise, contacts internal in selection 1 are considered. The Distance cutoff selects the radius to consider contacts in the native state. If only one selection is given, contacts can be filtered with the Δ resid option (see description in RMSD trajectory tool enhanced with native contacts). Group name specifies the label for two atom lists (that will be placed at the top of the plumed file). Note: After generating the CV lines, remember to set the top molecule to the one you want to analyze.
Backbone torsion CVs
A list of φ, ψ, and ω Ramachandran angles can be inserted for an atom selection. Note that N-CA-C atom names are assumed for backbone atoms. Dihedrals involving atoms outside the selection are not added. The ω angle is intended between residue i and i+1.
You need a driver executables for your architecture located somewhere in the path. The executables are named plumed (Plumed 2.0) and driver (Plumed 1.3). You can have either or both installed.
Windows the easiest is to download the pre-compiled binary for Win32 (version 1.3) and copy it e.g. in c:\windows or in VMD's directory. Users willing to compile the plugin themselves can see the windows build instructions. (Plumed 2.0 executable to come soon).
Linux users can download the code from PLUMED home page and build it following the instructions.
The path to driver's executable will appear in the "Path to executable" box; it can be adjusted manually if outside of the search path (not recommended).
By downloading the software you agree to comply with the terms of the 3-clause BSD license.
You are kindly requested to cite the following paper in any publication resulting from the use of Plumed-GUI (in addition to other possibly relevant Plumed citations):
Toni Giorgino, Plumed-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts (submitted)
Former support from the Agència de Gestió d'Ajuts Universitaris i de Recerca - Generalitat de Catalunya is gratefully acknowledged.