README file for VMD 1.9.2
---------------------------------------------------------------------------
What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/
---------------------------------------------------------------------
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 1.9.2?
------------------------
New Features and Performance Improvements
o Fast GPU-accelerated quality-of-fit cross correlation enables
analysis of results from molecular dynamics flexible fitting (MDFF)
and other hybrid structure determination methods:
http://dx.doi.org/10.1039/C4FD00005F
o New built-in TachyonL-OptiX GPU-accelerated ray tracing engine
speeds up high quality image and movie renderings, particularly
for scenes using ambient occlusion lighting and shadows:
http://dx.doi.org/10.1145/2535571.2535595
o VMD now includes a built-in implementation of the collective variables
feature also implemented in NAMD, enabling easier preparation
and analysis of NAMD simulations using collective variables:
http://dx.doi.org/10.1080/00268976.2013.813594
o Built-in support for parallel analysis and visualization using
MPI, with new VMD "parallel" commands:
http://dx.doi.org/10.1109/XSW.2013.10
o Added initial support for large scale parallel scripting with Swift/T:
http://www.ks.uiuc.edu/Research/swift/
o VMD supports off-screen OpenGL rendering, enabling large
scale parallel visualization runs on "headless" GPU clusters and
petascale computers, using a new "-dispdev openglpbuffer" flag:
http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=KLEI2014-JS
o An improved "QuickSurf" molecular surface representation allows
molecular dynamics trajectories to be animated for selections of
10,000 to over 1,000,000 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 100 million atoms
on machines with sufficient host and GPU memory capacity:
http://dx.doi.org/10.2312/PE/EuroVisShort/EuroVisShort2012/067-071
http://dx.doi.org/10.1145/2535571.2535595
o The improved QuickSurf implementation now supports visualization
of coarse-grained and cellular scale models:
http://dx.doi.org/10.1002/jcc.23130
http://dx.doi.org/10.1016/j.parco.2014.03.009
Other updates and improvements
o Added initial support for ARM processors and the Android OS
o Added support for compilation of VMD with Tcl 8.6.x
New and improved plugins and extensions
o Bendix: calculates and visualizes both dynamic and static
helix geometry, and abstracts helices without sacrificing conformation:
http://sbcb.bioch.ox.ac.uk/Bendix/
o FFTK: The 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
http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
o MDFF: added option in mdff setup to use implicit solvent
o NetworkView: a 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 normal mode analysis plugin
o psfgen: Add non-plugin NAMD binary file writing command "writenamdbin".
Properly handle insertion codes by appending the code to the
resid string as in "48A". Read and write insertion code in resid
field of psf file. Add "readpsf file.psf pdb file.pdb" to
read insertion code from pdb file. Add "regenerate resids" to
remove insertion codes with minimal residue renumbering.
Leave atoms in reasonable order when applying patches.
Do not generate O-H-H angles (assume these are water molecules).
Free old memory when regenerating angles or dihedrals for
entire structure. Handle masses as large as 99999.
Use 6-wide atom type when writing CHARMM EXT format X-PLOR psf file.
Use field width of 10 when reading CHARMM EXT
angles/dihedrals/impropers/cmaps.
o Remote: A plugin for managing VMD remote control connections
from mobile phones and wireless tablet devices
o Timeline: improved graphical interface with better zooming, and
improved display of very long timescale trajectories
o topotools: New topogromacs features,
allow support replication of non-orthogonal cells,
handle low-dimensional system box dimensions consistent with LAMMPS,
fix bug in writing non-orthogonal boxes reported by Sandeep Kumar Reddy,
add support for new Coeff section in LAMMPS data files,
add support for writing LAMMPS data files with triclinic cells.
o Modified TkCon to prevent it from sourcing command line args
as script files at startup.
New and improved file import and export
o cubeplugin: Make the parser for the cubefile header more resilient
when new fields are added like in g09 rev d.01.
o dcdplugin: Changed the dcdplugin reader code to avoid using readv()
to prevent problems when reading 240M-atom trajectories on some
versions of Linux.
o dlpolyplugin: Fixed a typo in the PBC unit cell basis vector
orthogonality check.
o gamessplugin: Fixed reading of minimization steps for recent
builds of Firefly 8
o gromacsplugin: Updates to gromacsplugin adding .gro write support,
contributed by Magnus Lundborg. Changed .gro parsing code to use
fixed field widths to address problems with files that had no
spaces between the coordinate fields.
o jslugin: Changed the jsplugin reader code to avoid using readv()
to prevent problems when reading 240M-atom trajectories on some
versions of Linux.
o lammpsplugin: Support LAMMPS native trajectories with variable
number of atoms through provisioning constant storage via an
environment variable LAMMPSMAXATOM.
Fixed bug in handling triclinic cells with negative tilt factors.
o maeffplugin: Fixed uninitialized optflags state in maeffplugin, so
that compilations that don't define DESRES_CTNUMBER will behave correctly.
o moldenplugin: Fixed various limitations that had previously
caused problems for Terachem users. Use case-insensitive string
comparisons when reading shell types from Molden files.
o molemeshplugin: Added Brian Bennion's plugin for reading mesh files
produced by MOLE 2.0.
o offplugin: Fixed internal initialization bug
o psfplugin: Handle various bond/angle/dihedral/improper
misformattings for 10M-100M-atom structures.
Made the PSF plugin allow NAMD-tagged PSF files to use a
space delimited bond record format since NAMD accepts that variation.
o rst7plugin: Added support for reading and writing box
and velocity information.
o tngplugin: Added support for the new Gromacs TNG plugin
o vtfplugin: Allow compilation of VTF plugin without Tcl,
updated to latest version by Olaf Lenz
o xsfplugin: Fixed a problem with the interpretation of the cell
vectors in cases that must be rotated.
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 parsefep: Updated ParseFEP docs with latest files from Chris Chipot.
o vdna: Updated Tom Bishop's contact info in the docs
Bug fixes and small improvements
o NetworkView: small GUI improvements and fixes
o fftk: fixes to GenZMatrix to allow for more general ACC/DON assignments
o Fixed a potential crash in the x86 SSE-accelerated version of the
wavefunction calculation for the Orbital representation
o Fixed an Interactive MD force cancellation bug that occured most
frequently when using Mouse-based control and multi-atom targets
o Fixed an old bug with 2-atom and 3-atom alignments
o Fixed a bug prevented clean compilations without Tcl,
needed for early Android testing.
o Updated the VMD copy of WKFThreads from the latest version of Tachyon.
Known bugs
----------
Visit the VMD page for information on known bugs, workarounds, and fixes:
http://www.ks.uiuc.edu/Research/vmd/
Cost and Availability
---------------------
VMD is produced by the The Theoretical and Computational Biophysics Group,
an NIH Biomedical Technology Research Center 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/gpu/
http://www.ks.uiuc.edu/Research/mdff/
http://www.ks.uiuc.edu/Research/namd/
http://www.ks.uiuc.edu/Research/vmd/
The VMD project is funded by the National Institutes of Health
grant numbers NIH 9P41GM104601 and P41-RR005969.
Disclaimer and Copyright
------------------------
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
-------------
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
-------------------------------
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
------------------
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 September 9, 2014 by John E. Stone