Important: please check the current version of software and. documentation at its home-page: http://www.multiscalelab.org/utilities/PlumedCVTool

A general collective variable analysis tool (PLUMED GUI)

The PLUMED collective variable analysis tool is a VMD plugin that provides access to the extensive set of collective variables (CV) defined in the [22]PLUMED software. It allows you to:

Please check that you have the latest version installed.

Usage

The usage of the plugin is straightforward.

  1. From VMD's main window, select "Extensions->Analysis->Collective variable analysis (PLUMED)"
  2. Edit the CV definition file, defining one or more CVs
  3. Enter the number of CVs defined in the corresponding box
  4. 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. The Edit menu provides the usual text-editing options.

Elements in the [23]Templates menu provides shortcuts for most CVs supported by PLUMED. Please refer to PLUMED's [24]user's guide for the full syntax.

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.

Reference structures for RMSD and path variables

The File->Prepare[25] 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: After generating the structures, remember to set the top molecule to the one you want to analyze.

Native contacts

The Edit->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 D resid option (see description in [26]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.

Batch analysis

Once a script is tested, the menu option File->Batch analysis... allows you to apply it to 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. You can set Number of processes to run multiple processes concurrently; it is advantageous to spawn between 1 and 2 times the number of CPU cores you have.

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 should to be set especially when dealing with non-wrapped solvent or with MD engines which "break" molecules by wrapping them. 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. Some options have not been included in the templates. Note that PLUMED's 1.2.0 parser for alignment structures is somewhat broken; workarounds are used, but feel free to apply the following patch to fix it permanently [32]patch-pdbparser. The plugin is current for PLUMED version 1.2.0.

Acknowledgments

(c) Universitat Pompeu Fabra 2010.

Author and feedback: Toni Giorgino (at gmail)

Work partially supported by the VPH-NoE.

[33]http://img191.imageshack.us/img191/496/vphlogo.png

Copyright 2008-2009. All rights reserved.

References

   Visible links
   1. http://www.multiscalelab.org/Welcome
   2. http://www.multiscalelab.org/utilities/PlumedCVTool?action=raw
   3. http://www.multiscalelab.org/utilities/PlumedCVTool?action=print
   4. http://www.multiscalelab.org/utilities/PlumedCVTool?action=AttachFile&do=view&target=patch-pdbparser
   5. http://www.multiscalelab.org/utilities/PlumedCVTool?action=AttachFile&do=view&target=vmdplumed.tcl
   6. http://www.multiscalelab.org/FindPage
   7. http://www.multiscalelab.org/TitleIndex
   8. http://www.multiscalelab.org/WordIndex
   9. http://www.multiscalelab.org/HelpOnFormatting
  13. http://www.multiscalelab.org/Welcome
  14. http://www.multiscalelab.org/Research
  15. http://www.multiscalelab.org/Software
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  17. http://www.multiscalelab.org/Publications
  18. http://www.multiscalelab.org/Contact
  19. http://www.multiscalelab.org/utilities/PlumedCVTool
  20. http://www.multiscalelab.org/utilities/PlumedCVTool?action=login
  21. http://www.multiscalelab.org/utilities/PlumedCVTool
  22. http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
  23. http://img204.imageshack.us/i/29948613.png/
  24. http://merlino.mi.infn.it/~plumed/PLUMED/Manual_and_Changelog_files/manual_1-2.pdf
  25. http://img835.imageshack.us/i/screenshotpreparerefere.png/
  26. http://www.multiscalelab.org/utilities/RMSDTTNC
  28. http://img836.imageshack.us/i/screenshotmultiplot.png/
  29. http://img204.imageshack.us/i/29948613.png/
  30. http://img835.imageshack.us/i/screenshotpreparerefere.png/
  31. attachment:vmdplumed.tcl
	http://www.multiscalelab.org/utilities/PlumedCVTool?action=AttachFile&do=view&target=vmdplumed.tcl
  32. attachment:patch-pdbparser
	http://www.multiscalelab.org/utilities/PlumedCVTool?action=AttachFile&do=view&target=patch-pdbparser