README file for VND
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What is VND? See also http://www.ks.uiuc.edu/Research/vnd/
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VND 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 VND can read
standard Protein Data Bank (PDB) files and display the contained
structure. VND provides a wide variety of methods for rendering and
coloring molecule. VND 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).
Known bugs
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Visit the VND page for information on known bugs, workarounds, and fixes:
http://www.ks.uiuc.edu/Research/vnd/
Cost and Availability
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VND 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/vnd/
The VND project is funded by the National Institutes of Health
grant numbers NIH 9P41GM104601 and P41-RR005969.
Disclaimer and Copyright
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VND is Copyright (c) 1995-2021 the Board of Trustees of the
University of Illinois and others. The terms for using, copying,
modifying, and distributing VND are specified in the file LICENSE.
The authors request that any published work which utilizes VND
includes a reference to the VND web page:
http://www.ks.uiuc.edu/Research/vnd/
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
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The VND Installation Guide, User's Guide, and Programmer's Guide
are available which describe how to install, use, and modify VND.
All three guides are available from the main web site.
Online help may be accessed via the "Help" menu in the main VND window
or by typing help in the VND command window. This will bring up the VND
quick help page in a browser, and will lead you to several other VND help
files and manuals.
Quick Installation Instructions
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Detailed instructions for compiling VND from source code
can be found in the programmer's guide.
The Windows version of VND is distributed as a self-extracting
archive, and should be entirely self explanatory.
The native MacOS X version of VND is packaged as a disk image and is
extracted by opening the disk image, and dragging the "VND" 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,
being sure to do this and subsequent steps as a non-root user.
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 vnd data files and executables should be installed, be sure
that you installing into a clean target directory and not overwriting
an existing version of VND (which would otherwise give problems):
$install_bin_dir is the location of the startup script 'vnd'.
It should be located in the path of users interested in running VND.
$install_library_dir is the location of all other VND 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,
become root or use sudo if necessary, e.g., for installation
of VND into /usr/local or other permission-protected system directories,
and type "make install". This will install VND 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 'vnd' to start (make sure the
$install_bin_dir directory is in your path).
Required Libraries
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VND 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 VND's optional features.
Please visit the VND web site for more information:
http://www.ks.uiuc.edu/Research/vnd/
For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'.
VND Development Team
Theoretical and Computational Biophysics Group
University of Illinois and Beckman Institute
405 N. Matthews
Urbana, IL 61801
TBG: https://www.ks.uiuc.edu/
VND: https://www.ks.uiuc.edu/Research/vnd/
README for VND; last modified June 21, 2021 by John E. Stone