VMD plugins at WMC Physiology & Biophysics

RMSDTT: RMSD Trajectory Tool

Description

The RMSDTT plugin is an improvement to the RMSD Tool plugin that can be found in the VMD distribution. The RMSDTT plugin adds support for rmsd calculations and alignment of trajectories, while retaining its old functionality. Two new options allow plotting of results via an external application, xmgrace (on unix systems) or Excel (on windows), and saving data to a file. The reference frame can also be specified.

• Version 1.7 added a new 'Trace' option and support for multi-line and comments in the atoms selection (see below).
• Version 1.8 adds support for Excel, new options to use time or frame as unit, and recovers the use of the average option for rmsd calculations of trajectories (not alignment). In this version, also a major change involves the use of the measure rmsd command instead of calculating the rmsd from scratch, and saves in memory usage.
• Version 1.9 adds partial support for all against all pairwise rmsd calculations. All frames will be compared against all frames in the trajectory. Support is only added for saving the data to a matrix, no plotting is supported at this time.
• Version 1.9.2.1 adds an option to exclude hydrogens from the atoms selection.
• Version 1.10 adds an option to skip frames.

In the previous figure the RMSD of trajectories md1 and md2 (200 frames each) is calculated with the xray as the reference (top molecule, 1 frame only). The RMSD Average are the mean for each trajectory, and the Overall Average RMSD is the mean of the three RMSD average values.

New options and changes:

• Trajectory activates the new plugin behavior. If not selected, the behavior is the same as with the RMSD Tool plugin.

• Frame ref sets the frame of reference for the reference molecule (Top or Selected). Added in version 1.9 is the option to calculate all against all pairwise rmsd when activating all.

• Skip allows skip frames in a regular fashion, starting from Ini and skipping every Steps. This feature was introduced in version 1.10.

• Time activates the use of time units (ps) has been introduced in version 1.8. Ini is the initial time, and Step in step size of each frame. This changes will be reflected in the plot and the output file.

• Plot will use xmgrace (on unix) or Excel (on windows, starting from version 1.8) to plot the data RMSD vs. frame. All xmgrace options and transformations can be used with the data; i.e. running averages, graph beautification, etc... VMD gives a warning message when exiting on windows systems if Excel is still open with data from VMD, but you still can continue using Excel. Xmgrace or Excel have to be installed on the system. Excel needs the tcom tcl library (see installation instructions).

• Save to file will save the data to the specified file. The format of the data is a table in which each row represents a frame and each column a molecule or trajectory. If the trajectories have differing numbers of frames, NA values are outputted. For example, the first frames in the previous example:

  frame       xray        md1        md2
      0  0.0000000  2.9420801  2.8631837
      1         NA  1.3335457  1.2748098
      2         NA  0.2971088  0.3996361
      3         NA  0.3294190  0.4151645
    ...        ...        ...        ...
  

• The Align button will also work with trajectories; i.e. in the last example all 200 frames of md1 and md2 would be fit onto xray. Note that the RMSD button has to be pressed again to obtain the new RMSD values after the alignment. The average option will not work with the Align.

• The Average option will work for calculating the RMSD in version 1.8, but not the alignment.

• The Trace will add 'and name CA' to the actual atoms selection. Note that since version 1.7 Backbone has been changed from it's VMD default to 'and name C CA N' (O is not included). In version 1.9.2.1 option noh has been added to exclude hydrogens from the atoms selection.

• The Multi-line atoms selection is a new and exciting feature introduced in version 1.7. The selection can now be split in different lines without affecting the final outcome. Also the character '#' can be used to comment out a portion of the selection, namely from the '#' to the end of that line (see figure above). Note also, that the record of an atoms selection in the history is not anymore done by pressing 'Return', but when pressing the 'RMSD' or 'Align' buttons.

Download

Installation

1. Download the plugin from here to the directory where you store your VMD plugins. Skip to point 4 if you are updating the plugin.
2. Add the following line to a file called pkgIndex.tcl in the same directory as the plugin (create it if it does not exists, or get it from here):

   package ifneeded rmsdtt 1.0 [list source [file join $dir rmsdtt.tcl]]

3. Add the following to your .vmdrc startup file (or create one) (for unix the path should be $HOME/.vmdrc, and for windows %USERPROFILE%\vmd.rc):
   1. For VMD 1.8.3 and up

      lappend auto_path {/path/to/your/plugins/directory}
      vmd_install_extension rmsdtt rmsdtt_tk_cb "WMC PhysBio/RMSDTT"
      

   2. For VMD 1.8.2 and down

      lappend auto_path {/path/to/your/plugins/directory}
      if { [catch "package require rmsdtt" msg] } {
        puts "VMD RMSDTT package could not be loaded:\n$msg"
      } elseif { [catch {menu tk register "rmsdtt" rmsdtt} msg] } {
        puts "VMD RMSDTT could not be started:\n$msg"
      }
      

   Remember to correct the path to your plugins directory; i.e, if you saved the plugin in /home/user/myplugins, write that same path in the auto_path line.

   Note: If you created the .vmdrc file, remember to add menu main on to get the main menu back.

4. Excel on Windows needs the tcom tcl library. Skip this step if you use unix. Download the library and install it (i.e. in your plugins directories). In general, only the tcom/lib/tcom directory is needed. Then add the following to your vmd.rc file:

   lappend auto_path {/path/to/tcom/lib/tcom}
   if { [catch "package require tcom" msg] } {
     puts "VMD tcom package could not be loaded:\n$msg"
   }
   

5. Start VMD. The RMSDTT plugin should be accessible from the Extensions menu.

Author

This plugin is based on the code of the RMSD Tool plugin, with modifications to some of its subroutines.

Send comments and feedback to Luis Gracia.