README file for VMD 1.9.2
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What is VMD?            See also http://www.ks.uiuc.edu/Research/vmd/
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  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 molecule.  VMD can be used to animate and analyze the trajectory 
of molecular dynamics (MD) simulations, and can interactively manipulate
molecules being simulated on remote computers (Interactive MD).

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

  o Many molecular and volumetric rendering and coloring methods.

  o Extensive atom selection language with boolean and algebraic operators, 
    regular expressions, distance based selections, and more.

  o Extensive graphical and text interfaces to Tcl, Tk, and Python 
    to provide powerful scripting and analysis capabilities.

  o High-quality on-screen rendering using OpenGL programmable shading on
    advanced graphics accelerators.

  o Stereoscopic display with shutter glasses, autostereoscopic flat panels,
    anaglyph stereo glasses, and side-by-side stereo viewing.

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

  o An extensible plugin-based file loading system with support for
    popular formats such as AMBER, CHARMM, Gromacs, NAMD, PDB, X-PLOR,
    and many others, as well as automatic conversion through Babel. 

  o Export displayed scene to external rendering formats including POV-Ray, 
    Raster3D, RenderMan, Gelato, Tachyon, Wavefront, as well 
    as STL or VRML2 files for 3-D printing.

  o Integration of multiple sequence alignment and evolutionary 
    analysis tools, in the form of the Multiseq plugin and its
    related toolset.

  o Perform interactive molecular dynamics (IMD) simulations using 
    NAMD, Protomol, or other programs as simulation back-ends.    

  o Integration with the program NAMD, a fast, parallel, and scalable
    molecular dynamics program developed in conjunction with VMD.
    See the NAMD page for details: http://www.ks.uiuc.edu/Research/namd

  o Integration with the BioCoRE collaborative research environment.
    VMD can "publish" molecular graphics scripts to BioCoRE, so that
    collaborators can work together over the internet.
    See the BioCoRE page for details: http://www.ks.uiuc.edu/Research/biocore


What's new in VMD 1.9.2?
------------------------
  Performance Improvements
    o The improved "QuickSurf" molecular surface representation allows 
      molecular dynamics trajectories to be animated for selections of 
      10,000 to well over 100,000 atoms depending on the speed of the 
      host machine.  Fast multi-core and GPU-accelerated implementations 
      of the QuickSurf representation enable faster/smoother 
      trajectory playback for moderate system sizes, and interactive 
      surface calculation for systems containing up to 20 million atoms 
      on machines with sufficient host memory and GPU memory.

  Other features and improvements
    o New test version of native 64-bit MacOS X port of VMD based on beta
      versions of Tcl 8.6 and FLTK for 64-bit MacOS X.
    o Updated VMD to use advanced GPU features in CUDA 4.0

  New and improved plugins and extensions
    o FFTK: The Force Field Toolkit (FFTK) plugin is a set of tools 
      that aid users in the development of CHARMM-compatible force 
      field parameters, including: charges, bonds, angles, and dihedrals
    o NetworkView: a plugin for the study of allostery and signalling
      through network models, allowing networks can be loaded and mapped onto 
      molecular structures loaded in VMD
    o NMWiz: A normal mode analysis plugin
    o Remote: A plugin for managing VMD remote control connections 
      from mobile phones and wireless tablet devices
    o Timeline: improved graphical interface with better zooming, and
      improved display of very long timescale trajectories 
    o Modified TkCon to prevent it from sourcing command line args 
      as script files at startup.

  New and improved file import and export
    o moldenplugin: fixed various limitations that had previously 
      caused problems for Terachem users.

  User documentation updates
    o Minor improvements and corrections to the VMD User's Guide,
      added documentation for new commands, graphical representations,
      and environment variables.
    o parsefep: Updated ParseFEP docs with latest files from Chris Chipot.
    o vdna: Updated Tom Bishop's contact info in the docs
 
  Bug fixes and small improvements
    o NetworkView: small GUI improvements and fixes
    o fftk: fixes to GenZMatrix to allow for more general ACC/DON assignments
    o Fixed a potential crash in the x86 SSE-accelerated version of the
      wavefunction calculation for the Orbital representation
    o Fixed an Interactive MD force cancellation bug that occured most
      frequently when using Mouse-based control and multi-atom targets
    o Fixed an old bug with 2-atom and 3-atom alignments
    o Fixed a bug prevented clean compilations without Tcl,
      needed for early Android testing.
    o Updated the VMD copy of WKFThreads from the latest version of Tachyon.

Known bugs
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  Visit the VMD page for information on known bugs, workarounds, and fixes:
    http://www.ks.uiuc.edu/Research/vmd/


Cost and Availability
---------------------
  VMD is produced by the The Theoretical and Computational Biophysics Group,
an NIH Biomedical Technology Research Center for Macromolecular Modeling 
and Bioinformatics, that develops and distributes free, effective tools 
(with source code) for molecular dynamics studies in structural biology.
For more information, see:
  http://www.ks.uiuc.edu/Research/biocore/
  http://www.ks.uiuc.edu/Research/gpu/
  http://www.ks.uiuc.edu/Research/mdff/
  http://www.ks.uiuc.edu/Research/namd/
  http://www.ks.uiuc.edu/Research/vmd/

The VMD project is funded by the National Institutes of Health
grant numbers NIH 9P41GM104601 and P41-RR005969.


Disclaimer and Copyright
------------------------
  VMD is Copyright (c) 1995-2011 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.

The authors request that any published work which utilizes VMD 
includes a reference to the VMD web page:
  http://www.ks.uiuc.edu/Research/vmd/

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.


Documentation
-------------
  The VMD Installation Guide, User's Guide, and Programmer's Guide 
are available which describe how to install, use, and modify VMD.  
All three guides are available from the main web site.
Online help may be accessed via the "Help" menu in the main VMD window 
or by typing help in the VMD command window.  This will bring up the VMD
quick help page in a browser, and will lead you to several other VMD help 
files and manuals. 


Quick Installation Instructions
-------------------------------
Detailed instructions for compiling VMD from source code
can be found in the programmer's guide.

The Windows version of VMD is distributed as a self-extracting 
archive, and should be entirely self explanatory.  

The native MacOS X version of VMD is packaged as a disk image and is
extracted by opening the disk image, and dragging the "VMD" application
contained inside into an appropriate directory.

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, be sure
     that you installing into a clean target directory and not overwriting
     an existing version of VMD (which would otherwise give problems):

     $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.  Similarly, if you have incorrectly
     specified the target installation directories or attempt to overwrite
     an existing VMD installation, you will get error messages.

  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:
  http://www.ks.uiuc.edu/Research/vmd/

For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'.
  VMD Development Team
  Theoretical and Computational Biophysics Group
  University of Illinois and Beckman Institute
  405 N. Matthews
  Urbana, IL  61801
  TBG: http://www.ks.uiuc.edu/
  VMD: http://www.ks.uiuc.edu/Research/vmd/


README for VMD; last modified October 18, 2012 by John E. Stone