README file for VMD 1.8.7
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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 extenal 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 1.8.7?
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User documentation updates
o Minor improvements and corrections to the VMD User's Guide,
added documentation for new commands and environment variables.
o Added documentation for new volmap ligand options, "measure pbc2onc",
and "measure pbcneighbors"
Performance Improvements
o Added support for NVIDIA CUDA on MacOS X, both
32-bit and 64-bit Linux, and Windows.
VMD supports CUDA acceleration for electrostatics calculations
(for both direct summation "volmap coulomb" and
multilevel summation method "volmap coulombmsm"),
for implicit ligand sampling, and for
acceleration of molecular orbital display.
o Added support for multi-core processors to the
Windows versions of VMD and the included Tachyon ray tracer
o Tachyon's ambient occlusion lighting performance has been
significantly improved with respect to the number of
ambient occlusion samples taken. The new version operates
multiplicatively with the number of antialiasing samples, so that
if one uses 12 antialiasing samples, only about 8 to 16
ambient occlusion samples are needed for good shading results.
General Improvements
o New graphical interface controls for shadow rendering and
ambient occlusion lighting have been added to the
Display Settings menu. Currently, these only affect renderings
with TachyonInternal, or Tachyon.
o Updated the nucleic acid structure analysis and ribbon/cartoon
representations to handle the new PDB atom names "OP1" and "OP2",
which have replaced the older "O1P" and "O2P" atom naming convention.
o Color selection menus reorganized into subcategories
New representations and display features
o New "PaperChain" and "Twister" graphical representations for
display of carbohydrate structures in VMD
o New "Polyhedra" representation for display silicon nanodevice
structures
o New "Orbital" representation displays and animates
molecular orbitals associated with the output of quantum chemistry
simulations
o New "outline" material property adds edge outlines on
drawn geometry. This material property is supported
with the GLSL interactive rendering mode, and for Tachyon renderings
o New ::vmd_pick_event callback for plugins to trace to get "pick" events
o PBC-aware trajectory smoothing
New and improved analysis commands
o General improvements of the plugin pbctools and a new function 'pbc
join' to join molecules that were broken due to wrapping over periodic
boundary conditions.
o new 'pbwithin' selection for selecting periodic neighbor atoms
within a cutoff distance
o new 'measure surface' command for finding surface atoms
o Added support for periodic boundary conditions to
the volmap implicit ligand sampling routines
o new 'measure pbc2onc' and 'measure pbcneighbors' commands.
o added three more demand-allocated per-timestep user-defined data fields
named "user2", "user3", and "user4",
Other features and improvements
o Added support for PowerPC based Linux for the Indiana 'BigRed'
Teragrid cluster
o Added support for Linux compilations using the Intel C/C++ compilers
o Secondary structure calculations using STRIDE are now able to
handle larger protein structures with up to 10,000 protein residues
and 100,000 atoms. Secondary structure calculations now propagate
error conditions if a STRIDE computation fails.
o Updated the py_numeric code for Python 2.5 and NumPy 1.x
o Updated the configure script to reference Python 2.5.x
o Greatly reduced the acceptable error tolerance for the RMS fitting
by default. The new tolerance is 1e-15, vs. the old tolerance which was
1e-5. The new code also accepts an environment variable
VMDFITRMSTOLERANCE which will override the default fit tolerance.
o Added support for an above/below stereo display mode for use with
special stereoscopic movie encoders
o Added recognition of SPC water.
New and improved plugins and extensions
o A new dynamic 'ruler' plugin for VMD for drawing ruled lines in 3-D
o New hydrogen bonds plugin for counting/plotting bonds over the course
of a molecular dynamics trajectory
o Updated the APBS plugin to allow dimension sizes n = a * 2^b + 1
for values of a other than 1.
o Updated vmdmovie plugin with correct transparency rendering flags
for movies made with Tachyon
o Updated the volmap plugin with support for the new
"Coulomb" potential map type
New and improved file import and export
o Updated bgfplugin with support for reading/writing
angles/dihedrals/impropers, and bug fixes.
o Updated ccp4plugin now reads and uses MRC2000 "ORIGIN" records
when available.
o Updated crdplugin now correctly reads trajectories that lack
line feeds between timesteps.
o Newly added dtrplugin reads Desmond trajectories, contributed
by D. E. Shaw Research.
o Improved compactness of ASCII-formatted DX files written by VMD
o Updated gamessplugin now reads wavefunction information, which can
be used to display molecular orbitals in VMD using the new
Orbitals representation.
o Updated lammpsplugin now supports newer style LAMMPS trajectories,
native LAMMPS text mode trajectories, adds support for many forms
of custom "dumps", and adds support for molecule ID, charges,
and velocities.
o Newly added maeffplugin reads structure files from
Schrodinger Inc's Maestro software, contributed by
D. E. Shaw Research.
o Updated mol2plugin with support for reading/writing
Antechamber bond orders, trajectories, and bug fixes.
o Updated msmsplugin to accept output from newer versions of MSMS
that emit comment lines at the top of the .vert and .face files.
o Updated parm7plugin to be more accepting of minor variations
in file structure so that VMD will read files written by other
AMBER-related software tools that don't strictly conform to the
output produced by the main AMBER tools.
o Updated pdbplugin now correctly clamps residue names to fit within
the fixed field width of the PDB format.
o Updated psfplugin to read and write angles/dihedrals/impropers and
cross-terms, for use by structure building tools.
o Updated situsplugin to add write support including the ability
to write orthogonal non-uniform cells by emitting a warning
and re-sampling the map on-the-fly.
o Updated version of vtfplugin by Olaf Lenz now supports loading and
saving more of the structure data in VMD.
o Updated xbgfplugin with support for reading/writing
angles/dihedrals/impropers, and bug fixes.
Bug Fixes
o Fixed a memory allocation bug with the 'within' distance selection
o Fixed Python callbacks
o Fixed memory leak in mol2plugin
o Fixed memory leaks in bgfplugin and xbgfplugin bond reading routines
o Fixed projection of surface normals into world coordinates
for isosurfaces of density maps with non-axis aligned basis vectors,
and/or opposite handedness coordinate systems.
o Fixed defaulted automatic color update behavior for coloring by
velocity, physical time, and user data per-timestep when
animating, or when using the draw multiple timesteps feature.
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 PHS 5 P41 RR05969).
Disclaimer and Copyright
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VMD is Copyright (c) 1995-2009 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 July 31, 2009 by John Stone