README file for VMD 1.5
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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 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.
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, Radiance, Raster3D, Rayshade,
and Tachyon.
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 outlining 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 interactively display and control an MD simulation
using NAMD.
What's new in VMD 1.5?
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New Features
o Support for several Gromacs structure and trajectory file formats:
- Can read .gro for structure (concatenated multiple-frame .gro
files are read automatically) (variable precision ASCII format)
- Can read .g96 for structure (concatenated multiple-frame .g96
files are read automatically) (fixed high precision ASCII format)
- Can read .trr for trajectory (full precision, portable binary format)
- Can read .xtc for trajectory (variable precision, compressed binary
format)
Note: Doesn't support .trj files, or combined run-input files yet, but
Gromacs users can run trjconv to convert these into one of the
formats that VMD can read.
o Windows versions of VMD now write their snapshot images as
24-bit color Windows Bitmaps (.bmp) files directly.
o Added the ability to modify the name, type, resname, resid
chain, and segname of a selection of atoms.
o Entirely new rendering capabilities implementing "material"
properties, for user control of ambient, diffuse, and specular
reflectivity, as well as surface shininess.
General Improvements and Bug Fixes
o Improved the rendering output for Raster3D and Tachyon
o General improvements to all renderer output.
o Major revision of IMD (Interactive MD) features in VMD.
o The Unix versions of VMD are now built with FLTK instead of XForms,
this brings both the Unix and Windows versions of VMD to using exactly
the same GUI, and decreases VMD's code/binary size noticably.
o New OpenGL code to allow SGI O2s to support stereoscopic display
with 16-bit depth buffering and and 12-bit color.
o Fixed quite a few of the outstanding problem reports (bugs)
that were sent in on previous versions of VMD.
PRs fixed: 5, 7, 10, 19, 23, 29, 58, 64, 68, 75, 76, 78, 79, 81,
83, 87, 88, 89, 90, 94, 95, 96, 97, 98, 100, 104, 105
o Rewrote large parts of the VMD display command system, yielding
some significant performance increases.
o Improvements to VMD's built-in help for various commands, better
help topic listings.
User Interface Changes
o New GUI color scheme, using lighter colors which are easier on most
people's eyes, particularly with laptops, projectors, etc.
o New "Mouse" form which supercedes the old "popup menu" found in
all of the previous Unix versions of VMD. The Mouse menu is
identical on both Windows and Unix, unlike the previous versions of
VMD where the Windows version had no analog to the popup menu.
o New "Materials" form which provides controls over rendering
properties for representations. (controls for shininess,
diffuse, ambient and specular reflectivity etc)
o Renamed the "Mol" and "Sim" forms to their longer names for increased
intuitiveness to new users.
o New "Cancel" button on the Molecule form providing the ability to
cancel loading of very large trajectory files.
User Documentation Updates
o Improved HTML version of documentation (new rev of latex2html)
o Improved PDF version of documentation, now uses better scalable fonts
o Updated the VMD tutorial to cover new GUI features
o The user guide does more to cover issues specific to the Windows
versions of VMD in better detail.
o Updated docs on rendering to snapshots and to external renderers
o Many updates to sections explaining the VMD GUI, particularly
the new GUI features.
Known bugs
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Please visit the VMD web site for information on known bugs,
workarounds, and fixes:
http://www.ks.uiuc.edu/Research/vmd/
Cost and Availability
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VMD, NAMD, and BioCoRE 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:
http://www.ks.uiuc.edu/Research/VMD/
http://www.ks.uiuc.edu/Research/NAMD/
http://www.ks.uiuc.edu/Research/biocore/
The VMD project is funded by the National Institutes of Health
(grant number PHS 5 P41 RR05969).
Disclaimer and Copyright
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VMD is Copyright (c) 1995-2000 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:
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
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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/ig.ps".
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
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Detailed instructions for compiling this version of VMD can be found
in the installation guide, ig.ps. 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
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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 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 June 28, 2000 by John Stone