From: jrhau lung (
Date: Thu Dec 01 2016 - 02:04:04 CST

Dear John:
       Thank you for all your efforts and kindly sharing.



2016-12-01 15:30 GMT+08:00 John Stone <>:

> Dear VMD-L,
> 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
> ---------------------------------------------------------------------
> 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
> 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:
> 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:
> files/pap110.pdf
> 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
> o lammpsplugin:
> 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.
> Known bugs
> ----------
> 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.
> 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,
> 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).
> 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:
> For problems, questions, or suggestions, send e-mail to ''.
> VMD Development Team
> Theoretical and Computational Biophysics Group
> University of Illinois and Beckman Institute
> 405 N. Matthews
> Urbana, IL 61801
> TBG:
> VMD:
> 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
> Phone: 217-244-3349