README file for VMD 1.9.1
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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 trajectory 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 High-quality on-screen rendering using OpenGL programmable shading on
advanced graphics accelerators.
o Stereoscopic display with shutter glasses, autostereoscopic flat panels,
anaglyph stereo glasses, and side-by-side stereo viewing.
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 external rendering formats including POV-Ray,
Raster3D, RenderMan, Gelato, Tachyon, Wavefront, as well
as STL or VRML2 files for 3-D printing.
o Integration of multiple sequence alignment and evolutionary
analysis tools, in the form of the Multiseq plugin and its
related toolset.
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 1.9.1?
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New rendering and display features
o New "QuickSurf" molecular surface representation allows molecular
dynamics trajectories to be animated for selections of
10,000 to well over 100,000 atoms depending on the speed of the
host machine. Fast multi-core and GPU-accelerated implementations
of the QuickSurf representation enable faster/smoother
trajectory playback for moderate system sizes, and interactive
surface calculation for systems containing up to 20 million atoms
on machines with sufficient host memory and GPU memory.
o Updated all VMD graphical representations to use new
atom selection traversal optimizations for faster trajectory animation,
particularly when animating subsets of very large structures.
o Improved export of representation group hierarchy and
material properties to Wavefront .obj files.
Performance Improvements
o The performance of atom selection operations has been significantly
increased for common cases where a subset of atoms (e.g. solute atoms)
are selected, in a fairly contiguous index range. This benefits the
performance of most selection operations, measure commands,
atom selection queries, and mouse-based picking and selection operations.
o Greatly improved the responsiveness of the VMD graphical interface
when loading over 2,000 molecules at a time.
o VMD now supports un-buffered disk I/O to allow large structure
files and trajectories to be read at rates of up 2 GB/sec on
fast SSD disk arrays.
o Linux versions of VMD are now compiled using the Intel C/C++
compilers, enabling SSE and various autovectorization performance
improvements.
Other features and improvements
o New test version of native 64-bit MacOS X port of VMD based on beta
versions of Tcl 8.6 and FLTK for 64-bit MacOS X.
o Updated VMD to use advanced GPU features in CUDA 4.0
o Increased default CAVElib and FreeVR shared memory allocation to 2 GB.
o Updated the FreeVR arena allocation code to try and loop over
arena sizes if the initial allocation fails
o Improved default FreeVR wand position offset and coordinate scaling
New and improved plugins and extensions
o CGTools: Added support for group rotation to optimized
reverse coarse graining
o FFTK: The new Force Field Toolkit (FFTK) plugin is a set of tools
that aid users in the development of CHARMM-compatible force
field parameters, including: charges, bonds, angles, and dihedrals
o HeatMapper: A new plugin for displaying 3-D plots in a 2-D "heat map"
o NetworkView: A new plugin for the study of allostery and signalling
through network models, allowing networks can be loaded and mapped onto
molecular structures loaded in VMD
o NMWiz: A new normal mode analysis plugin
o Molefacture: Added +4 oxidation state for sulphur
o Multiseq: Allow non-redundant set calculations with marked sequences,
corrected handling of non-standard residues in ClustalW and MAFFT calls
o ProPKA: A new graphical interface to allow results from ProPKA runs to
be interactively displayed in VMD
o Remote: New plugin for managing VMD remote control connections
from mobile phones and wireless tablet devices
o RMSD Visualizer: A new plugin for computing and plotting RMSD and RMSF
values for selected atoms over trajectories
o Timeline: improved graphical interface with better zooming, and
improved display of very long timescale trajectories
o Modified TkCon to prevent it from sourcing command line args
as script files at startup.
o ViewMaster: Added new procedures to get the next and previous views,
relative to the current view that is being shown, in support of
the VMD remote control plugin, so that the VMD Aux-event keys can
trigger viewmaster to cycle through a slideshow.
New and improved file import and export
o Updated the cross-platform fast I/O routines used by molfile plugins
to support direct un-buffered I/O for high performance access to
SSDs and SSD RAID arrays on the Linux and Windows platforms.
o Enabled automatic compilation of plugins that use sqlite and libexpat.
o dmsplugin: Latest version contributed by D.E. Shaw Research.
o dtrplugin: Latest version contributed by D.E. Shaw Research.
o hoomdplugin: Updated to latest version.
The HOOMD plugin is compiled by default on Linux and MacOS X.
o gamessplugin: Added support for Firefly log files, improved
support for PC-GAMESS
o jsplugin: Support for fast un-buffered I/O, enabling
2 GB/sec streaming trajectory read rates on fast SSD arrays.
o lammpsplugin: Added optional support for dipolar particles by
translating them into two atoms around the center with the distance
scaled by the value stored in LAMMPSDIPOLE2ATOMS, which also enables
this feature. recognize more field types in preparation for the
second part of the update. Update output format to the current style.
Added support for element, mass and diameter field.
Improve handling of periodic box output.
o maeplugin: Latest version contributed by D.E. Shaw Research.
o mol2plugin: updated to align decimal points in charge column
o moldenplugin: Added support for "(AU)" in units strings emitted by
Molcas, added support for alternative forms of scientific notation in
basis set coefficients.
o msmsplugin: Added floating point code to workaround issues with
floating point emulation in the Microsft compiler toolchain.
o offplugin: New OFF reader plugin contributed by Francois-Xavier Coudert
o psfplugin: Add support for new NAMD-specific formats for structures
containing very long atom names and types, e.g. CGenFF models.
o stlplugin: Added floating point code to workaround issues with
floating point emulation in the Microsft compiler toolchain.
User documentation updates
o Minor improvements and corrections to the VMD User's Guide,
added documentation for new commands, graphical representations,
and environment variables.
o chirality: Added citation now that the paper describing this plugin
is published.
o cispeptide: Added citation now that the paper describing this plugin
is published.
Bug fixes and small improvements
o Fixed Python material change tuple argument format list
o Fixed bugs in FreeVR button/tracker subclass initialization, and
button assignment in the latest revs of FreeVR.
o Corrected references to material files when exporting Wavefront OBJ
files on the Windows platform.
o cionize: Updated cionize Makefile for latest CUDA and Intel C/C++
compilers for the iccgpuionize64 target.
o irspecgui: Corrected bug when reading charges from external file.
o molefacture: Fixed calculation of formal charge for R1-(PO4-)-R2.
Fixed a bug to correctly find "C*" atom types in the OPLS parameter file.
o multiseq: Revised unknown residue conversion code to use X for
unknown residues if amino acids; N if nucleic.
o mutator: Fix inconsistencies in mutator version numbers, and cranked
to next version for recent updates.
o namdenergy: Improved the efficacy of the "silence" option.
Fixed the behavior of the "-updatesel" flag.
o paratool: Fix call to non-existent "hesstrans" proc so it
calls "hessiantransform".
o psfgen: Made the psfgen segment generation output slightly more compact.
Cause psfgen to prepend "psfgen) " to all of its console output.
o qmtool: fixed reading of ESP charges for later versions of Gaussian
o rmsdtt: Updated RMSD Trajectory Tool GUI to report 4 digits for
molecule IDs.
o runante: Improved handling of antechamber errors for poor structures.
Fix to make sure bonds are written to antechamber input files.
Fixed bug when checking for Antechamber executable.
o runsqm: Fixed bug in ::runsqm::sqminit when checking for sqm executable.
o solvate: Modified solvate to print estimated completion times at most
only once every 30 seconds rather than during generation of every
replica. Updated the solvate plugin to better handle generation of very
large solvent boxes. We now check the maximum segment name length
that will result from the required number of replicas, and use
either decimal, hexadecimal, or base-26 alphanumeric segment
naming schemes depending on which one will most easily fit into
the 4-character field width limit of the oldest PSF/PDB file formats.
Improved the diagnostic messages.
o topotools: Guessing element from mass was off.
Added guess name from type and made element lookups case insensitive.
Use resid for the molecule id on writing, since this is what
we read in. Corrected output format for hybrid atom style.
o timeline: Fixed bad error condition that could occur when no results
could be produced by a calculation.
o viewchangerender: Updated to fix small GUI bugs.
o vmdmovie: Fixed a bug in the movie maker plugin that prevented movies
from being created correctly for Windows users.
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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VMD is produced by the The Theoretical and Computational Biophysics Group,
an NIH Resource 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/biocore/
http://www.ks.uiuc.edu/Research/namd/
http://www.ks.uiuc.edu/Research/vmd/
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 P41-RR005969).
Disclaimer and Copyright
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VMD is Copyright (c) 1995-2011 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.
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 1, 2012 by John E. Stone