VMD README file
---------------
See the end of this file for quick information on installing the program VMD.

                         NOTE FOR FTP USERS
                         ------------------
The VMD ftp directory (ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/) contains
several different versions of the VMD distribution, in two compression
formats.  Files ending in '.gz' have been compressed with the GNU 'gzip'
utility, while files ending in '.Z' have been compress with the standard
Unix 'compress' program.  Please copy the '.gz' versions if you have gzip
available; if you do not have gzip, get the '.Z' version.  There are two
forms of VMD available:
	1) vmd.all.tar.gz (or .Z) : the complete distribution, with source
           code, documentation, and a precompiled binary for IRIX 5.X machines
	2) vmd.bin.tar.gz (or .Z) : does not include the source code or
           extra libraries ... but this does include the documentation and a
           precompiled binary for IRIX 5.X machines

What is VMD?
------------
VMD is designed for the visualization 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 Many molecular rendering and coloring methods.
        o Stereo display capability.
        o Extensive atom selection syntax for choosing subsets of atoms for
          display (includes boolean operators, regular expressions, and  
          more).
        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 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, Rayshade, and Raster3D.
        o Extensive graphical and text-based user interfaces, which use the
          Tcl package to provide full scripting capabilities.
        o Modular, extensible source code using an object-oriented design in
          C++, with a programmers guide describing the source code structure.
        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 info:  
                  http://www.ks.uiuc.edu:1250/Research/namd

          VMD can be used to set up and concurrently display a MD simulation
          using NAMD.  The two programs, along with the intermediary
          communcations package (called MDComm) constitute the 'MDScope'
          environment.  

Availability
------------
VMD runs on Silicon Graphics workstations and may be compiled
for HP-UX workstations if the NPGL library (a commercial port of the GL
library, available from Portable Graphics, Inc.) is available on your system.
Two versions of the distribution are available, one including the complete
VMD source code, and one which just includes a precompiled VMD executable for
SGI IRIX version 5.

The source code and documentation for VMD are freely available for
noncommercial use from the Theoretical Biophysics anonymous ftp server, in
the directory /pub/mdscope/vmd:
		ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/

VMD, NAMD, and the entire MDScope environment are part of an ongoing project
within the Theoretical Biophysics group to help provide free, effective tools
for structural biology research.  This project is funded by the National
Institutes of Health and the National Science Foundation.

Documentation
-------------
The VMD distribution includes three documentation files in postscript format.
These manuals document how to install, use, and modify VMD.  The manuals
found in 'doc' directory of the distribution are:
	1) An installation guide (doc/ig.ps)
	2) A users guide (doc/ug.ps)
	3) A programmers guide (doc/pg.ps)

A quick help file in HTML format, 'vmd_help.html' is also available, in the
'data' directory of the distribution.  This file may be viewed by any HTML
viewer, and is used to provide on-line help for VMD when it is running.

For the latest information on VMD, please see the VMD WWW home page:
		http://www.ks.uiuc.edu:1250/Research/vmd/
This page contains links to HTML versions of all three VMD manuals
listed above, and info on the latest release of the program.  A (very)
brief VMD FAQ is also available, and can be found either by looking
at the VMD home page, or directly via the URL:
		http://www.ks.uiuc.edu:1250/Research/vmd/vmd_faq.html

Installation
------------
Instructions for installing this version of vmd can be found 
in the installation guide, doc/ig.ps.  For a quick installation,
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.parameters'; change the value for
the INSTALLLIBDIR to a directory in which vmd data files and executables
should be installed, and change the value for INSTALLBINDIR to a directory 
where the utility programs and startup script should be placed (INSTALLBINDIR 
should be a directory in the path of users interested in running vmd).

A) **********  IF YOU ARE INSTALLING VMD FOR SGI IRIX version 5.X  ***********

The distribution includes a precompiled version of VMD for IRIX 5.X, which
will run only on Silicon Graphics workstations with IRIX 5.X or later installed.
If this is the case, follow the next steps, otherwise skip to point B) below.

	3) Generate a Makefile to be used to install vmd by entering the
command:
		configure

	4) change to the 'src' directory, and enter the command:
		make install
	
	5) When installed, type 'vmd' to start.


B) **** IF YOU ARE INSTALLING VMD FOR SGI IRIX version 4.X, or HP-UX 9.X ****

VMD must be compiled before installation; to do so, follow these steps:

	3) The proper Makefile must be generated for your architecture and
preferred options.  For now, run the configure script with these options, 
based on the type of OS being used (if you do not have the Tcl libraries
available, omit the word TCL from the following commands):
	for IRIX 4.X:  configure IRIX4 GL FORMS TCL UNC OPTIMIZE
	for IRIX 5.X:  configure IRIX5 GL FORMS TCL UNC REMOTE OPTIMIZE
	for HPUX 9.X:  configure HPUX9 GL FORMS TCL OPTIMIZE
	               (Note: To run on HPUX, the NPGL library
				from Portable Graphics must be installed
				in /usr/local/npgl, to provide a version
				of the GL library used for the graphics.)

	4) After configuration is complete, cd to the src directory,
and type 'make depend; make'.  This will compile the program into an executable 'vmd_<architecture>'

	5) After compilation is finished, enter the command:
		make install

	6) When installed, type 'vmd' to start.


For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'.

	W. Humphrey, A. Dalke, K. Hamer, J. Leech, J. Phillips
	Theoretical Biophysics Group
	University of Illinois and Beckman Institute
	405 N. Matthews
	Urbana, IL  61801
	TBG WWW: http://www.ks.uiuc.edu
	VMD WWW: http://www.ks.uiuc.edu/Research/vmd/


General README for VMD; last modified 6/28/95 by WFH
