README file for VMD 1.8.3
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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 seelections, 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 1.8.3?
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User Documentation Updates
o Source code documentation is provided online and is updated nightly.
o Extensive updates to the VMD Tutorial have occured for the new version
User Interface Changes
o New controls and text commands for changing label text size
o The defalt behavior of the isosurface representation slider is to
calculate an isosurface with half as many samples per axis while the
slider is being dragged, providing a much faster interactive rendering
rate, followed by a full resolution isosurface computation when the
slider is released. In cases where it is desirable to get a full
resolution isosurface as it is being adjusted, holding down any of
the shift/ctrl/alt keys will force VMD to calculate the isosurface at
full resolution even while dragging the slider.
o Isosurface reps are automatically created (with box) when volume data
is loaded into a new molecule (rather than lines).
o The color scale range can be customized for the "Index" coloring method
New Features
o New APBS electrostatic potential interface plugin
o New Camera Navigator plugin allows the user to fly the camera
using the keyboard in perspective projection mode.
o New Clipping Plane plugin provides a simple interface to manipulate
the 6 user-defined clipping planes to one, all active, or all molecules.
o New Multiple Alignment plugin performs sequence and structure alignments
on molecules loaded in VMD.
o New PMEpot Particle Mesh Ewald potential map calculation plugin
o New graphical interface for Solvate plugin
o New ViewMaster plugin provides an easy-to-use interface for
managing multiple molecular views, saving them, and switching between
them.
o New "Volume" coloring method, for use with electrostatic potential maps,
and other volumetric datasets. Requires OpenGL 1.2 3-D texture mapping.
o New "NewCartoon" secondary structure representation draws better
looking structures than the original cartoon representation and
animates faster for trajectory playback.
o New "measure sasa" command to measure solvent accessible surface area
for an atom selection.
o New "color restype" command to override the default assignment of
residue types used for coloring by residue type.
o Windows version of VMD now supports MSMS surface representations
o Windows versions of VMD now support 3-D texturing used by the
"VolumeSlice" representation, and the new color by "Volume" feature.
o New "display cachemode" command and matching Display menu controls,
enable whole-molecule display list caching in VMD, which can yield
significant performance improvements when rendering over a network
or on tiled display systems, or when rendering large static structures
with high triangle counts such as isosurfaces.
o New "display rendermode" command and matching Display menu controls
provide a nicer way to switch into and out of the special
alpha-blended transparency and GLSL rendering modes.
o Preliminary support for OpenGL shading language (GLSL).
VMD shaders will continue to be updated over time, the first
implementation is now workable, though it has various limitations.
New and improved file import and export
o Significantly improved Tachyon and POV-Ray output for MSMS surfaces,
NewRibbons, and other triangulated surface geometry.
o All molecular geometry can now be exported to external renderers that
support triangle primitives.
o New Wavefront OBJ renderer format for use with tools such as Maya
o New DLPOLY formatted HISTORY file reader plugin
o New Insight II/Discover "car" reader plugin
o New LAMMPS molecular dynamics trajectory reader plugin
o New PQR file reader/writer plugin
o New SYBYL "mol2" reader plugin
o New Tinker "arc" reader plugin
o New Molecular Discovery GRID volumetric map reader plugin
o Significantly improved the Amber 7.x parm plugin with rewritten code
o Updated Charmm coordinate file reader plugin addressing a bug
o Updated Gaussian Cube plugin to read non-orthogonal unit cells
o Updated PSF structure file reader plugin to read PSF files
created by CNS 1.1
o Updated XYZ plugin to parse files containing atomic numbers rather
than string-based atom names.
o Significant DCD trajectory reader performance improvements
o The DCD trajectory reader/writer plugin has been udpated to fix
a byte swapping problem on Charmm trajectories containing fixed atoms,
and now writes files in Charmm/NAMD format by default including
unit cell information.
o Updated the DX reader plugin to fix a potential problem reading
grid lengths, and to use friendlier volume dataset names
o Updated the Gromacs readers to allow periodic cells with zero-length
periodic cell dimensions
o Updated brixplugin, ccp4plugin, edmplugin, and fs4plugin fixing a bug
in handling non-orthogonal cells.
o All plugins now use common byte swapping code for greatly increased
performance reading opposite-endian binary files. In actual use,
this results in byte-swapped DCD trajectory reading performance of
up to 294MB/sec on high-end workstations, with medium-range
machines achieving 100MB/sec from local disks.
General Improvements and Bug Fixes
o 20-fold performance increase when rendering volume slice representations
on most graphics accelerators.
o More than tripled the peak read performance large trajectory
files using the "waitfor all" option compared with previous versions.
o The 'vmdmovie' plugin now generates movies much more quickly
due to new features implemented by the Snapshot and InternalTachyon
renderers and improved image format conversion logic.
o The 'vmdmovie' plugin now supports the use of POV-Ray for ray tracing
of movies
o Numerous AutoIMD improvements make it more usable on local workstations
and more easily configurable to local clusters and queueing systems.
o Atom selection 'set' operations now perform at peak speed without
the need to disable display updates or other performance tricks.
o Significantly improved the 'points' isosurface representation,
selected better defaults for the isosurface representation.
o Atom selection performance improvements for "name" and arithmetic
evaluation selections.
o Better range checking when writing PDB files from molecules in VMD
o Eliminated string copy of residue indices
o The Windows joystick code now emits user key events for button presses.
o The "FPS" indicator's color can now be changed in the Color window.
o Corrected the position of user-defined clipping plane origins
o Faster picking performance over networks
o Bond search code now tolerates wildly out-of-scale atom coordinates and
handles unusual situations much better. Minimal error messages are
printed now, and crashes should not be possible now.
o The 'delete trajectory frames' GUI now behaves as one would expect
rather than the strange frame selection logic used in past versions.
The stride parameter now specifies the frames to _keep_:
deleting 0 to 9 with a stride of 4 will keep frames
0 4 8, instead of the old behavior 1 2 3 5 6 7 9.
o The 'vmd' startup script for Linux now correctly auto-detects the
appropriate binary to run on x86 and x86_64 Linux distributions.
o Enhanced the shutdown process to allow plugins and scripts to
terminate cleanly if they have callbacks and such.
o Updated Contact Map and Timeline plugins with improved user interface
code. Cleaned up the user interface.
o Improved built-in help for various text commands
o Fixed problems that occured with psfgen and very long filenames
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) 1995-2005 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 February 14, 2005 by John Stone