README file for VMD 1.8.5
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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 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 animation 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 Stereoscopic display with shutter glasses, autostereoscopic flat panels,
anaglyph stereo glasses, and side-by-side stereo viewing.
o High-quality on-screen rendering using OpenGL programmable shading on
advanced graphics accelerators.
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 extenal rendering formats including POV-Ray,
Raster3D, Renderman, Tachyon, Wavefront, as well as STL or VRML2 files
for 3-D printing.
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 1.8.5?
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General Improvements
o MacOS 10.4 versions for PowerPC and Intel processors support
quad-buffered stereoscopic display on Macs with Quadro 4500
graphics cards (or similarly capable hardware).
o New MultiSeq 2.0 multiple sequence alignment plugin replaces the
multiple alignment plugin, and allows both structure based sequence
and pure sequences to be aligned and analyzed
o Support for VRPN 7.03, lower cost HDAPI-based haptic devices
User documentation updates
o MultiSeq 2.0 documentation has been added
o APBS plugin docs include a short tutorial on coloring solvent
surfaces by potential
o Significantly expanded documentation for users interested in developing
extensions and plugins in Tcl/Tk, Python, and C/C++.
o Minor improvements and corrections to the VMD User's Guide,
added documentation for new commands and environment variables.
User interface changes
o "RWB" is now the default color scale (previously "RGB")
o New min/max range controls for isosurface representation isovalue slider
o The materials menu is now populated with a much larger set of
materials by default.
o OpenGL Shading language compiler diagnostic errors are now printed
only when the VMDGLSLVERBOSE environment variable is set.
New representations and display features
o NewCartoon representations now draw nucleic acid structures with
ribbons for the backbone and cylinders for each nucleotide
o Significant improvements for display of nucleic acids using the existing
NewRibbons and NewCartoon representations
o Dynamic reclalculation of bonds can now be set for several additional
atom-oriented representations, for use with trajectory playback
o Pick points can now be created for user-defined graphics, to allow
the creation of completely customized graphics and behaviors using
the scripting interfaces.
o The built-in color table and menus now contain 32
user-modifiable base colors rather than the old limit of 16.
o Atom labels can now be displayed with user defined format strings,
and with a defined offset from the atom coordinate.
o Added new "RGryB" and "BGryR" color scales for use when coloring
by potential on white backgrounds
o New VMDMACENABLEEEXTENSIONS environment variable enables
performance-oriented OpenGL extensions which trigger bugs
on some Mac systems.
o New VMDSHEARSTEREO environment variable enables an alternative
perspective projection mode for improved stereoscopic display
o New VMDIMMERSADESKFLIP environment variable enables a special
reversed/reflected stereo projection mode for use with experimental
displays based on LCD panels, phase plates, and beam splitters.
New analysis commands
o New 'measure dipole' command for calculating dipole moments
o New 'measure gofr' command for calculating radial pair distribution
functions
o New 'mol reanalyze' command allows one to force VMD to completely
re-analyze the molecular structure due to changes in atom names,
residue names, bonding/topology, etc. This is intended to be used by
structure building tools and other special applications where one wishes
to change the structure on-the-fly.
New and improved plugins and extensions
o New MultiSeq 2.0 multiple sequence alignment plugin replaces the
multiple alignment plugin, and allows both structure based sequence
and pure sequences to be aligned and analyzed
o New BioCoRE collaboration plugins for chatting,
remote file system access, remote job submission, and VMD state exchange
o New "Virtual DNA" visualization plugin can display a graphical
representation of DNA according to its helical parameters (no atomic
structure)
o New "g(r)" graphical interface for radial pair distribution
function calculation and plotting
o New IR spectral density calculation and plotting tool
o New representation cloning visualization plugin makes it easy to
copy a set of representations from one molecule to another
o New Palette Tool visualization plugin displays active colors
and materials, for test rendering and printing
o Molefacture plugin now allows structures to be built from scratch using
a library of fragments and residues
o New Salt Bridge plugin finds salt bridges that form over a trajectory
o New CGTools plugin for converting between coarse grain
and all-atom models
o New 'NavFly' mouse-based flying camera navigation plugin
o Mutator plugin now includes support for free energy perturbation
o APBS plugin now includes a mobile ion editor, and
supports job remote execution
o NAMDEnergy plugin now supports remote job execution
o Extended the exectool plugin with support for remote job submission
through BioCoRE
o Improved the clipping plane tool user interface
o Improved Color Scale Bar plugin now has better range controls,
improved behavior with white backgrounds, and generally more robust.
o Improved Ramachandran plotting plugin includes a new 3-D time averaged
histogram display feature.
New and improved file import and export
o New VASP plugins read atomic configurations, trajectories,
charge density and electron localization function volumetric grids.
o AMBER file readers now convert to/from elementary charge units
o Improved Gromacs plugin now reads TRJ trajectory files
o Improved column alignment in mol2plugin mol2 file writing routines
o Improved LAMMPS plugin now reads more structure data out of trajectories
Bug Fixes
o Fixed a potential crash when 'measure contacts' was used with a
very very small distance parameter, on very large structures
o Fixed a potential crash in the labels window when molecules were deleted
o Fixed a memory leak in the atomselect 'moveby' subcommand
o Fixed a potential crash in the 'atomselect macro' command
o Fixed the state saving script so that it correctly saves and restores
the user-defined clipping planes. Also made the state loader more
robust so that any color settings errors don't abort the loading
process, and will continue on with remaining color settings.
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
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BioCoRE, JMV, MDTools, NAMD, VMD and the Structural Biology Software
Database represent the broad efforts of the Theoretical and Computational
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/biocore/
http://www.ks.uiuc.edu/Research/namd/
http://www.ks.uiuc.edu/Research/vmd/
http://www.ks.uiuc.edu/Research/jmv/
http://www.ks.uiuc.edu/Development/biosoftdb/
http://www.ks.uiuc.edu/Development/MDTools/
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) 1995-2006 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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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
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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
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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 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 August 21, 2006 by John Stone