PLUMED collective variable analysis tool

The PLUMED collective variable analysis tool VMD plugin provides convenient access to the extensive set of collective variables (CV) defined in the PLUMED software. It allows you to:

interactively edit META_INP files and plot CVs on the currently loaded trajectory
use VMD atom selection keywords to define atom groups
quickly insert templates for common CVs
export the CV definition file for use in MD simulations
prepare reference files for RMSD and path-variable computations
batch processing of multiple DCD files

Usage

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
Click "Plot". This will open a plot window with the selected CVs.

CV definition files can be opened, edited and saved as usual. Save and Save as... save the currently open file varbatim, while the Export.. function performs the atom selection replacements (see below), thus creating a META_INP file that can be used directly in simulations. For the syntax of PLUMED input files, refer to its user's guide.

Square brackets can be used to conveniently define atom groups. During evaluation, atom selection keywords in square brackets are replaced with a list of the corresponding serial numbers for the top molecule. (Note that you still have to embed them in the PLUMED group definition syntax.)

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.

Elements in the ''Templates'' menu provides shortcuts for most CVs supported by PLUMED. Note that many options are not been included in the template; please refer to PLUMED's user guide for the full syntax. The Electrostatic energy and Dipole CVs require charges to be defined in the currently loaded molecule (i.e., AMBER or CHARMM topology file have to be loaded beforehand).

The menu option File>Batch analysis... allows you to process all of the DCD files in a chosen directory. The files are processed according to the current settings, and need to match the top molecule. If the Combine option is unselected, a .dcd.colvar file will be created along with each .dcd trajectory. If the Combine option is selected, the metrics for the various trajectories will be joined in a single metric.dat file. Lines of the file contains the file name, followed by the usual COLVAR columns (without header). Note: existing .colvar or metric.dat files will be overwritten without warning.

The ''Edit>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. Note that PLUMED's 1.2.0 parser for alignment structures is broken (the plugin uses workarounds); apply the following patch to fix it patch-pdbparser.

Notes. The number of CVs defined has to be entered manually. In case of errors, inspect the console; it will provide diagnostics and the location of the temporary files. Hills deposition should be disabled. Periodic boundary conditions need to be set if dealing with non-wrapped solvent or with MD engines which "break" molecules by wrapping them.

Screenshot

User interface:

Installation

Locate the scripts folder under your VMD installation directory and create a directory named init.d (if not already there).
Download the plugin source and copy it in the newly-created directory.
Place PLUMED's driver in your system's search path.

Prerequisites. The plugin requires that you have PLUMED's driver utility installed. If the executable is not in the path, its location should be specified in the "Options" box.

The plugin is current for PLUMED version 1.2.0.

Licensing

By downloading the software you agree to comply with the terms of GPL version 2.

Acknowledgments

Work partially supported by the VPH-NoE.