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) : contains the binaries for VMD and
     MDComm, the VMD startup scripts, and some documentation.

  These names will always point to the most current announced version
of VMD, which at this time is VMD 1.1 .

What is VMD? (see also http://www.ks.uiuc.edu/Research/vmd/)
------------
  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 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, Raster3D, and Radiance.
        o Extensive graphical and text-based user interfaces, which use the
          Tcl package to provide full scripting capabilities.
        o Extensions to the Tcl language which enable researchers to write
           their own routines for molecular analysis
        o Modular, extensible source code using an object-oriented design in
          C++, with a Programmer's 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/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 SGI
GL library, available from Portable Graphics, Inc.) is available on
your system, or to IBM 6000s with GL.  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.x.  A nearly complete OpenGL implementation compatible
with Mesa is available as part of the source distribution, but VMD does
not yet compile with g++.

  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 molecular dynamics studies in structural biology.
For more information, see http://www.ks.uiuc.edu/Research/MDScope/.
This project is funded by the National Institutes of Health and the
National Science Foundation.

Disclaimer and Copyright
------------------------

    VMD is Copyright (c) 1995-1996 Theoretical Biophysics Group and
the Board of Trustees of the University of Illinois

    This program is free software but is not in the public domain.  It
is distributed in the hope that it will be useful to the molecular
modelling community, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.  Should the software prove defective YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

Permission is granted for research, educational, and commercial use
and modification so long as 1) VMD and any derived works are not
redistributed for a fee, 2) proper credit is given to the Theoretical
Biophysics group for their work, and 3) programs derived from VMD
must by given a different name.  If you use VMD in a way you think
is interesting or novel, we would like to know about it.

Some of the code and executables used by VMD have different
restrictions.  They are:

1) STRIDE, the program used for secondary structure calculation, is
free to both academic and commercial sites provided that STRIDE will
not be a part of a package sold for money.  The use of STRIDE in
commercial packages is not allowed without a prior written
commercial license agreement.  See
http://www.embl-heidelberg.de/stride/stride_info.html.

2) Det, Eigen, and Invert are part of the LASSTools package from
Cornell.  See http://www.lassp.\\cornell.edu/LASSPTools/LASSPTools.html.
The executables may be redistibuted to other users.  Note that this
redistribution may not be done for a fee (other than a material media
charge, if necessary).  Ownership resides with the authors of the
programs.

3) The source code for SURF is copyrighted by the original author,
Amitabh Varshney, and the University of North Carolina at Chapel Hill.
Permission to use, copy, modify, and distribute this software and its
documentation for educational, research, and non-profit purposes is
hereby granted, provided this notice, all the source files, and the
name(s) of the original author(s) appear in all such copies.

BECAUSE THE CODE IS PROVIDED FREE OF CHARGE, IT IS PROVIDED "AS IS" AND
WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.

This software was developed and is made available for public use with
the support of the National Institutes of Health, National Center for
Research Resources under grant RR02170.

See ftp://ftp.cs.unc.edu/pub/projects/GRIP/SURF/surf.tar.Z .

4) The perl script to retrived web documents, url_get, was written by
Jack Lund at the University of Texas as Austin.  There appear to be
no restrictions on its use.

See http://uts.cc.utexas.edu/\~zippy/projects/url_get/ .

5) Several parts of the GNU C++ class library are used in VMD,
including the String and Regex classes, alloca, and librx regular
expression library.  As per the GNU General Public License v. 2, the
modified code is available as part of the general \VMD\ source
distribution and may be freely used and altered.


Feedback
--------

  We would like to know who is using our software both for our own
knowledge and to support our funding.  If you find VMD useful or
want to make comments, please fill out our on-line feedback form at
http://www.ks.uiuc.edu/Research/vmd/VMDfeedback.html .

Documentation
-------------
  Three postscript documentation files are available for VMD which
describe how to install, use, and modify VMD.  One, the installation
guide, is contained in the VMD distribution in the file doc/ig.ps .
The other two, the User's Guide and Programmer's Guide are available
independently from the VMD distribution directory as ug.ps and
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.  This file does not contain information about version
1.1 .

For the latest information on VMD, please see the VMD WWW home page:
             http://www.ks.uiuc.edu/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
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/Research/vmd/vmd_faq.html

Installation
------------
Detailed instructions for installing this version of vmd can be found 
in the installation guide, 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) go to step 7


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

VMD must be compiled before installation but it is STRONGLY advised
that A) you use the installation guide (ig.ps), B) you know something
about compiling and installing programs, and C) you have Tcl, Tcl-X, and
XForms installed.  If you are courageous:

	5) 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 SURF UNC OPTIMIZE
	for IRIX 5.X:  configure IRIX5 GL FORMS TCL SURF UNC REMOTE OPTIMIZE
	for AIX  3.X:  configure AIX3 GL FORMS TCL SURF
	for HPUX 9.X:  configure HPUX9 GL FORMS TCL SURF 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.)

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


	7) change to the 'src' directory, and enter the command:
		make install

	8) go to the INSTALLIBDIR directory then
		cd scripts/vmd

        9) edit the first line of 'url_get' to point to the perl 
interpreter on your system.  This is usually /usr/local/bin/perl but
could be /usr/sbin/perl .  If perl is not installed, don't worry, the
only thing it is important for are the three commands which can download
information over the network (specifically, "url_get", "mol urlload", and
"mol pdbload").
	
	10) When installed, type 'vmd' to start (make sure the installation
directory is in your path).


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 5/14/96 by Andrew Dalke.

