VMD

Visual Molecular Dynamics (VMD)

VMD is a good visualization tool for visualizing large molecular systems (typically used for large biomolecular systems). VMD has a long history of being interfaced to immersive technologies, including haptic devices and CAVE VR displays. There is also a section on the usage of VMD for HPC systems.

Immersive Mode VMD

Information specific to the usage and setup of VMD for immserive systems such as the CAVE virtual reality display.

How to Run VMD in Immersive Mode

If VMD with the FreeVR interface is installed and properly configured, follow these steps to run in immersive mode:

1. % module load freevr vmd
2. % vmd -dispdev freevrforms <path>/proteins/brH.pdb
   • This alone should be sufficient to render the molecule in the VR system, with joystick-controlled travel
3. In order to grab and move an object, the grab tool must be initialized:

   1. →Graphics →Tools
   2. →Create a grab style tool
   3. set Position to FreeVRTracker
   4. set Buttons to FreeVRButtons

   The wand avatar will now appear in the scene

4. Now touch an object with the wand avatar and press Button-1 to move it.

How to Configure VMD for Immersive displays

There are two stages of configuration required for the overall configuration of VMD for immersive displays. The first step is to configure FreeVR for the specific hardware setup of the immersive facility. This is explained in the FreeVR documentation. The second stage is to link the FreeVR inputs to VMD "sensors devices".

VMD "sensor devices" are specified in the .vmdsensors file. The format of this file is described in the VMD User's Guide: Tool Window documentation.

• Create a .vmdsensors file in your $HOME directory or the local directory:

  Here is a sample .vmdsensors file for use with FreeVR:

###     
### Configuration for the FreeVR trackers
###     
device freevrtracker freevrtracker://local/freevr
scale 0.5
offset 0.9 -4.0 -1.0
device freevrbuttons freevrbuttons://local/freevr:0,1,2,3
## uncomment the following if you have more than one wand:
#device vrtracker2 freevrtracker://local/freevr:1
#scale 1.0
#offset 0.9 -4.0 -1.0

How to Build VMD w/ Immersive features

This section specifically instructs on how to compile VMD using the FreeVR immersive interface library.

1. Install missing dependencies

   Commonly needed packages include:

   • tcl-devel (8.5 -- 8.6 works with edits to Makefile)
   • tk-devel (8.5 -- 8.6 works with edits to Makefile)
   • fltk-devel
   • netcdf-devel

2. Download the latest source (version 1.9.4a57 as of this writing [12/21/23])

   http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

   NOTE: there is a (free) registration process required

   NOTE: the pre-built packages may not contain the Immersive features

3. Untar the source ball

   E.g. % tar -zxf vmd-<version>.src.tar.gz

   (As of this writing [12/21/23] <version> is 1.9.4a57)

4. Compile the plugins

   % export PLUGINDIR=`pwd`/vmd-<version>/plugins

   % cd plugins

   Ensure the Makefiles are set for the proper version of Tcl/Tk:

   % $EDITOR ./cionize/Makefile.specialbuilds ./Make-arch ./Make-arch.debug

   CHANGE: edit tcl8.5 and tk8.5 to be tcl8.6 and tk8.6 respectively if that's the version of Tcl/Tk installed on your system

   % make <architecture> — E.g. LINUXAMD64

   % make distrib

5. Configure VMD

   % cd ../vmd-<version>

   % $EDITOR configure.options

   Enter a list of desired options -- make sure to include FREEVR

   A sample list is:

   • LINUXAMD64 OPENGL FREEVR FLTK TK TCL PTHREADS

   An expanded list is:

   • LINUXAMD64 OPENGL OPENGLPBUFFER FREEVR FLTK TK CXX11 XINERAMA XINPUT LIBPNG ZLIB VRPN NETCDF TCL PTHREADS SILENT

   (I don't necessarily know what all those do and whether they help or not)

   (As of this writing [12/21/23] I was unable to get the CUDA, Optix or Python options to work.)

   % $EDITOR configure

   CHANGE: install_bin_dir=<installation-path>/bin

   CHANGE: install_library_dir=<installation-path>/lib/$install_name

   % ./configure

6. Compile VMD

   % cd <path>/vmd-<version>

   % export PLUGINDIR=`pwd`/plugins — only if you're in a different shell from where this happened in step 4

   % cd src

   % $EDITOR Makefile

   CHANGE: edit the values for INCDIRS and LIBDIRS to point to the correct directory for the FreeVR includes and library.

   • (UNLESS: you've configured $CPATH and $LPATH, perhaps through the "modules" system.)

   CHANGE: edit tcl8.5 and tk8.5 to be tcl8.6 and tk8.6 respectively if that's the version of Tcl/Tk installed on your system

   • NOTE: Ideally the VMD build system would just specify tcl8 and tk8.

   * make veryclean

   % make -j 8

   NOTE: you will get a handful compiler warnings. As long as they are only warnings, you should be fine.

7. Install VMD

   % sudo make install

At this point you can now run VMD in standard desktop mode.

• For example:

  % vmd ../proteins/brH.pdb

General Usage

Usage Tidbits

• To place the FLTK menu interface on a screen separate from the immersive displays, use the DISPLAY environment variable prior to running the vmd command.

• To change the overall world transformation via the Tcl command shell, try these options:
  • vmd > scale to .5
  • vmd > translate to 0 0 -3
  • vmd > rotate y by 5

• To modify the atomic/molecular representation:
  • vmd > mol modstyle 0 0 CPK; puts "CPK"
  • vmd > mol modstyle 0 0 Licorice; puts "Licorice"

• To modify selected objects:
  • vmd > set a [atomselect 0 all]
  • vmd > set xval 4
  • vmd > set yval 2
  • vmd > $a moveby [list $xval $yval 0]

• To connect VR and other inputs to TCL scripts:
  • vmd > user add key Aux-5 { scale by 1.3 }
  • vmd > user add key Aux-7 { scale by 0.7 }
  • vmd > user add key Aux-6 { animate forward; puts "play" }
  • vmd > user add key Aux-8 { animate forward; puts "pause" }
  • vmd > user add key Aux-0 { mol modstyle 0 0 CPK; puts "CPK" }
  • vmd > user add key Aux-1 { mol modstyle 0 0 Licorice; puts "Licorice"

• To add new objects/annotations into the world:
  • vmd > graphics top text { 0 0 0 } "hello"
  • vmd > graphics top cone { 40 0 0 } { 40 0 10 } radius 10 resolution 60
  • vmd > graphics top line { 10 0 0 } { 0 0 0 } width 5 style dashed
  • vmd > graphics top list — output a list of object IDs (I think)
  • vmd > graphics top info 1 — or any of the ID numbers returned in the list

• Useful system commands:
  • vmd > logfile console &mdash start recording interactions as TCL commands (like ParaView's trace)
  • vmd > logfile off — stop the TCL command trace and output the results
  • vmd > menu main off — or on
  • vmd > menu list — list all the interface menus
  • vmd > user print keys — list all the keyboard shortcuts

• To get information about the environment:
  • vmd > vmdinfo arch
  • vmd > echo $auto_path — lists the path whence plugins are searched

• Commands that aren't useful in Immersive Mode:
  • vmd > display resize 1920 1080
  • vmd > display projection orthographic

Usage Issues

[NOTE: these issues are from tests with VMD version 1.9.2a15. (And need to be re-tested with version 1.9.4a57)]

• I still need to figure out the proper scale and offset (this would/will be easier if we can avoid the use of Euler angles in P_GrabTool.C).
• The grab tool only grabs one molecule object at a time, so multiple molecules won't stay together.
• The grab tool requires that the wand avatar be touching an object before it can be moved.
• The rotate tool does not work
• I don't know how to use the joystick tool — does it work with the VR interfaces?
• I need to learn whether (and if so what) the command-line and/or tcl-shell options for setting up the graphics tools w/o the need for the interactive menu.
• There are gimble lock issues when the wand points up or down.
• The material colors of some/all of the objects in the scene are not always present.
• Changes in representations seem to only have an effect on a single screen.

Build Issues

• VMD should compile with Tcl/Tk 8.6 (as mentioned above), probably better to just use the major version number
• The CUDA option did not compile for me as it's hard-coded to Cuda version 10.2, and I have version 12.3.
• Some of the plugins report as being broken when starting VMD -- but some of them work, so it's not a matter of improperly building/installing the "plugins".

Development Issues

This section is for issues that are of interest to those working directly on the VMD code-base as it relates to immersive interfaces.

• DONE: Need to figure out how to pass RenderInfo * argument to FreeVRScene::draw() in order to add the navigation controls to where the virtual world is rendered.
• Need to go over the source code in P_GrabTool.C so that I can know how to improve it (and I'll add comments as we go.) My goal is to avoid the use of Euler angles, since there are gimble lock issues in the interface.
• Consider adding a grab-world tool that allows the entire world to be grabbed with the wand. An alternative was done — an always active "Grab-World" operation.
• Determine whether there is a mechanism to enable an X11 window always-on-top property for the FLTK control menu.
  • Alternatively, a command that returns the X11 id of a menu's window could be used by a tool like xdotool to manipulate the window however is desired.

Non-immersive development issues

• Can FLTK menus work without OPENGL enabled?
• Running ./configure should report installation directories — since those are options we may want to change (otherwise one may not know where these can be configured).
• Is there a command (if not, can one be added) that reports the configuration options of the compiled VMD?
• "Lines" and "Points" representations don't seem to work when rendering from BigRedII to the desktop.
  • (I don't care about the BigRedII HPC system anymore, but this issue may also exist when using VNC, etc.)

HPC Usage of VMD

This section describes specific usage and compiling issues related the VMD on HPC systems such as the Indiana University BigRedII supercomputer.

Running VMD via command-driving interactions on BigRedII

Presently, the VMD installed on BigRedII can be used interactively via the TCL command language. Once running in an interactive shell, a molecule can be loaded and rendered with these simple commands:

1. Load the vmd module:

   % module load vmd

2. Start VMD:

   % vmd

3. Load an example molecule:

   vmd > mol new <path>/brH.pdb

4. Render the current "view" to an image file:

   vmd > render TachyonInternal <filename>.ppm

5. Quit VMD

   vmd > quit

Then, perhaps in another shell, an image viewer program can be used to see the rendered text. [NOTE: this requires logging on from an X11-cabable desktop system and using the -X flag to ssh.]

• Use the FEH image viewer:

  % module load imlib2 feh

  % feh --reload 1 <filename>.ppm

• or use the Eye-of-Gnome viewer:

  % eog <filename>.ppm

Links to Old Immersive Mode VMD wiki pages

Here are links to previous versions of this page that were designed for older VMD releases:

• VMD 1.9.1 instructions (April 2014)