README file for VMD 1.7.1

What is VMD?            See also
  VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies,
etc.  It may be used to view more general molecules, as VMD can read
standard Protein Data Bank (PDB) files and display the contained
structure.  VMD provides a wide variety of methods for rendering and
coloring a molecule: simple points and lines, CPK spheres and
cylinders, licorice bonds, backbone tubes and ribbons, and others.
VMD can be used to animate and analyze the trajectory of a molecular
dynamics (MD) simulation.  In particular, VMD can act as a graphical
front end for an external MD program by displaying and animating a
molecule undergoing simulation on a remote computer.

The program has many features, which include:
  o No limit on the number of molecules, atoms, residues or
    number of animation frames, except available memory.

  o Many molecular rendering and coloring methods.

  o Stereoscopic display capability using Red/Blue or LCD shutter glasses.

  o 3-D interactive control through the use of joysticks, spaceballs,
    haptic devices and other advanced input, including support for the 
    UNC Virtual Reality Peripheral Network (VRPN) system.

  o Extensive atom selection syntax for choosing subsets of atoms for
    display (includes boolean operators, regular expressions, and more).

  o Ability to write the current image to a file  which may be 
    processed by a number of popular raytracing and image rendering
    packages, including POV-Ray, Radiance, Raster3D, Rayshade, 
    and Tachyon.

  o Integration with the program 'Babel' which allows VMD to read many
    molecular data file formats.  Even without the use of Babel,
    VMD can read PDB files, as well as CHARMM- and X-PLOR compatible
    binary DCD files and X-PLOR compatible PSF files.

  o Extensive graphical and text-based user interfaces, which use
    Tcl, Tk, and Python to provide powerful scripting capabilities.

  o Built-in extensions to the Tcl and Python languages which enable 
    researchers to write their own routines for molecular analysis.

  o Modular, extensible source code using an object-oriented design in C++.

  o Integration with the program NAMD, a fast, parallel, and scalable
    molecular dynamics program developed in conjunction with VMD
    in the Theoretical Biophysics Group at the University of Illinois.
    See the NAMD WWW home page for more information:

  o VMD can be used to interactively display and control an MD simulation
    using NAMD or Protomol.    

  o Integration with the BioCoRE collaborative research environment.
    VMD can "publish" molecular graphics scripts to BioCoRE, so that
    BioCoRE collaborators can work together over the internet.
    See the BioCoRE WWW home page for more information:

What's new in VMD 1.7.1?
  New Features
    o New volume rendering features including isosurface display,
      volume slicing with support for hardware accelerated 3-D 
      texture mapping, and a Tcl volume data loader interface.
    o Support for scanline-interleaved stereoscopic rendering for 
      hardware such as the Eye3D stereo glasses and decoders.
      These work on Linux, Windows, and most any other platform with
      VGA and USB connectors, and they don't require any special software
      in order to work with VMD.
    o First inclusion of VMD plugin architecture.  Initially used
      to provide the structure building capabilities of psfgen 
      in VMD.
    o Added "mol selupdate" and "$sel update" commands.  "mol selupdate" '
      causes automatic updates of the selection for the specified 
    o The Windows version of VMD can now be run from a command line 
      with the use of the Windows "start" command, i.e. something like
      "start c:\vmd\vmd.exe -nt -e myscript.vmd" could be used to 
      start VMD if it were installed in directory c:\vmd.

  General Improvements and Bug Fixes
    o Includes a much faster version of Stride for secondary structure 
    o Includes new version of the Tachyon ray tracer, 0.93.4.
    o Multi-level OpenGL stipple-based "screen door" transparency.  Now
      implements varying levels of transparency.
    o Improved support for WireGL cluster-based rendering and tiled display
    o The IMD code now closes down active socket connections more 
      carefully, allowing the kernel to complete any in-progress
      write operations before closing the socket.
    o POV-Ray scene export improved with new camera parameters and
      support for orthographic views, shadow control, and matched 
      perspective camera views.
    o Tachyon scene export improved with new camera parameters for 
      matched perspective views with VMD.
    o Raster3D scene export improved with new camera parameters for
      matched perspective views with VMD.
    o The Windows version of VMD now reads "vmd.rc" for startup instead
      of ".vmdrc".  This makes it much easier to edit the startup files
      on Windows.
    o Replaced DNA example molecule with a better one.
    o H-bonds shown in the H-bond rep are now pickable.
    o Added code to read the unit cell data from Charmm trajectory files.
    o Improved robustness and error handling when reading Raster3D 
      scene files.  Fixed Raster3D file reading crash.
    o The "delete" option for atom selections no longer leaks memory
      in the case when it is used within a Tcl loop.  
    o Eliminated atom selection and Tcl related memory leaks 
    Fixed Bugs and PRs: 107, 168, 170, 171, 172, 173, 174, 177, 178

  User Interface Changes
    o Users can select either FLTK or Tk file browsers according to
      their personal preference.  Some people prefer the Windows-like
      function of the Tk browsers, while others like the filename 
      completion of the FLTK file browser.  This is configured by setting
      the VMDFILECHOOSER environment variable.  The default browser for
      Windows is the Tk browser, for Unix systems the FLTK browser is 
      the default.
    o Reverted behavior of the edit form old "-1" index use.

  User Documentation Updates
    o New manual section for the sequence window
    o Updated sections regarding .vmdrc since Windows now uses vmd.rc instead.
    o Updated the betacolor example script included in the docs for 
      new versions of VMD.
    o Updated the animation scripts in the script library for new
      versions of VMD.
    o Improved index entries pertaining to lighting and shading.

Known bugs
  Please visit the VMD web site for information on known bugs, 
  workarounds, and fixes:

Cost and Availability
  BioCoRE, JMV, MDTools, NAMD, VMD and the Structural Biology Software
Database represent the broad efforts of the Theoretical Biophysics Group, 
an NIH Resource for Macromolecular Modeling and Bioinformatics, designed 
to develop and distribute free, effective tools (with source code) for 
molecular dynamics studies in structural biology.  
For more information, see:

The VMD project is funded by the National Institutes of Health
(grant number PHS 5 P41 RR05969).

Disclaimer and Copyright
  VMD is Copyright (c) 1995-2001 the Board of Trustees of the 
University of Illinois and others.

The terms for using, copying, modifying, and distributing VMD are
specified in the file LICENSE. If you use VMD in a way you think is
interesting or novel, we would like to know about it.

The authors request that any published work which utilizes VMD 
includes a reference to the VMD web page:

and/or the following reference:

  Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
  Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

  Three VMD manuals are available which describe how to install, 
use, and modify VMD.  The VMD installation guide, is contained in 
the VMD distribution in the file "doc/". 
The User's Guide and Programmer's Guide are available separately 
(due to size) from the VMD web site.  Quick help may be accessed
by pressing the "Help" button on the main VMD form, or by typing
help in the VMD command window.  This will bring up the VMD
quick help page, and will lead you to several other VMD help files
and manuals. 

Quick Installation Instructions
The Windows version of VMD is distributed as a self-extracting 
archive, and should be entirely self explanatory.  Detailed instructions 
for compiling this version of VMD can be found in the installation guide.  
For quick installation of the binary distribution for Unix do the following:

  1) uncompress and untar the distribution into a working directory.
     In this working directory, there are several subdirectories such 
     as bin, src, doc, data, as well as this README and a configure script.  
     Change to this working directory after the unpacking is complete.

  2) Edit the file 'configure'; change the values for
     the $install_library_dir and $install_bin_dir to a directory in 
     which vmd data files and executables should be installed:

     $install_bin_dir is the location of the startup script 'vmd'.  
     It should be located in the path of users interested in running VMD.

     $install_library_dir is the location of all other VMD files.  
     This included the binary and helper scripts.  It should not be 
     in the path.

  3) A Makefile must be generated based on these configuration variables
     by running "./configure". 

  4) After configuration is complete, cd to the src directory,
     and type "make install".  This will install VMD in the two
     directories listed above.  Note that running "make install" 
     twice will print error messages because you are attempting to 
     overwrite some read-only files.  This should be fine.

  5) When installed, type 'vmd' to start (make sure the
     $install_bin_dir directory is in your path).

Required Libraries
  VMD requires several libraries and programs for various of its functions.
In particular, it uses GL or OpenGL based 3-D rendering, and will require
that you have the appropriate GL or OpenGL libraries on your system.  
Other programs are required by some of VMD's optional features.
Please visit the VMD web site for more information:

For problems, questions, or suggestions, send e-mail to ''.

  VMD Development Team
  Theoretical Biophysics Group
  University of Illinois and Beckman Institute
  405 N. Matthews
  Urbana, IL  61801

README for VMD; last modified December 23, 2001 by John Stone