VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 01 2016 - 01:30:55 CST
I've just posted the first batch of final VMD 1.9.3 release builds on the
web site. The new version includes many new features, and a variety
new plugins and tools contributed by many members of the VMD user community.
In a few days I will add some additional release builds for some of
the new hardware platforms after a little extra testing is done for
the special cases.
A brief summary of new features in VMD is included below:
README file for VMD 1.9.3
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 scene file formats including POV-Ray,
Raster3D, RenderMan, Tachyon, Wavefront OBJ, as well as STL, VRML2, or
X3D files for 3-D printing.
o Integration of multiple sequence alignment and evolutionary
analysis tools, in the form of the Multiseq plugin and its
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
What's new in VMD 1.9.3?
New platform support:
o Added support for Cray XC50 supercomputers with NVIDIA Tesla P100 GPUs.
o Support for Intel Xeon Phi Knight's Landing CPUs with AVX-512
vector instructions, specifically targeting early science projects
running on the TACC Stampede-2 and ALCF Theta supercomputers:
o Support for IBM POWER8 CPUs and the new "Minsky" compute node
that incorporates NVIDIA Tesla P100 GPUs attached via NVLink,
for the upcoming ORNL CAAR early access system:
o Support for a range of ARM processors paired with GPUs:
New Features and Performance Improvements
o New QwikMD integrative MD simulation tool guides users in
preparing, running, and analyzing MD simulations:
o Automated Topology Conversion from CHARMM to GROMACS with
the topotools plugin "topogromacs" feature:
o New TachyonL-OSPray ray tracing engine for Intel x86 and Xeon Phi
CPUs (including Knights Landing aka KNL) speeds up high quality image
and movie renderings, particularly for scenes using ambient occlusion
lighting and shadows.
o Faster TachyonL-OptiX GPU-accelerated ray tracing engine
supports rendering of VR movies for YouTube with display
by Google Cardboard, GearVR, Oculus Rift, etc:
The new version also speeds up high quality image and movie renderings,
particularly for scenes using ambient occlusion lighting and shadows:
o VMD supports off-screen OpenGL rendering with both traditional
GLX (with a windowing system) and with EGL (without a windowing system),
enabling large scale parallel visualization runs on "headless"
clouds, clusters, and petascale computers, using the
"-dispdev openglpbuffer" flag:
Other updates and improvements
o Improved the robustness of the QuickSurf representation for display
of very large biomolecular complexes such as viruses, coarse grained
models, and corrected behavior for some unusual structures.
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:
o VMD 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:
o Built-in support for parallel analysis and visualization using
MPI, with VMD "parallel" commands:
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
o Bendix: calculates and visualizes both dynamic and static
helix geometry, and abstracts helices without sacrificing conformation:
o Modified TkCon to prevent it from sourcing command line args
as script files at startup.
o Updated support for compilation of VMD with Tcl 8.6.x
New and improved file import and export
o pdbxplugin: support for the RCSB PDB "PDBx" format.
o ccp4plugin: support for many new IMOD tomography voxel formats
o vtkplugin: New VTK grid reader plugin
o raster3dplugin: Patch to correct the Raster3D reader plugin for
some Molscript output files that previously didn't work right
Replaced the quicksort based index sorting with a mergesort,
thereby avoiding the worst-case O(N^2) quicksort performance
pitfall that arises when it is presented with an already-sorted list.
Eliminated compiler warnings on missing return value from
internal id_merge() function.
o babelplugin: Updated minor version number to reflect alternate code
paths added to the VMD directory/path traversal code in vmddir.h
o dtrplugin: Applied patch to cause the dtrplugin code to use
PRIu64 macros rather than hard-coded format conversion specifiers when
scanning or printing 64-bit values for various internal quantities.
o graspplugin: Eliminated test for negative value on an
unsigned integer type.
o parmplugin, parm7plugin: Prevent code injection attacks
on the auto-decompression code path.
o gamessplugin: Corrected uninitialized pointer.
o offplugin: Added support for handling of Windows line breaks
and a suspicious index check.
o vaspxmlplugin: Correction for null termination of string.
o maeffplugin: Correction to console exception reporting case.
o moldenplugin: Correct an uninitialized pointer.
o jsplugin: Auto-enable SSD-optimized unbuffered block-based I/O for
all structures with more than 50,000 atoms, for which alignment
padding overhead for on-disk and in-memory data structures are
under 1% on average. Emit more diagnostic information in cases where
the Linux kernel returns errors and does not do partial writes.
o dcdplugin: eliminate compiler warning on IBM Power8
o dlpolyplugin: Updated dlpoly plugin support DLPOLY V4 history files,
and to make a distinction between classic DLPOLY files and those
produced by DLPOLY V4.
o plyplugin: Misc cleanup and bug fixes for the PLY plugin
User documentation updates
o Minor improvements and corrections to the VMD User's Guide,
added documentation for new commands, graphical representations,
and environment variables.
Bug fixes and small improvements
o fftk: misc small bug fixes.
o Updated the VMD copy of WKFThreads from the latest version of Tachyon.
Visit the VMD page for information on known bugs, workarounds, and fixes:
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:
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) 1995-2016 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:
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.
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,
being sure to do this and subsequent steps as a non-root user.
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,
become root or use sudo if necessary, e.g., for installation
of VMD into /usr/local or other permission-protected system directories,
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).
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:
For problems, questions, or suggestions, send e-mail to 'vmd_at_ks.uiuc.edu'.
VMD Development Team
Theoretical and Computational Biophysics Group
University of Illinois and Beckman Institute
405 N. Matthews
Urbana, IL 61801
README for VMD; last modified November 29, 2016 by John E. Stone
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/