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:
- 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
Please check that you have the latest version installed.
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. 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
16. http://www.multiscalelab.org/People
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