VMD 1.9.3 beta1 Released!

greatzdk

What's new in VMD 1.9.3?
------------------------
  New Features and Performance Improvements
    o New QwikMD integrative MD simulation tool:
      http://dx.doi.org/10.1038/srep26536
    o Automated Topology Conversion from CHARMM to GROMACS with
      the topotools plugin "topogromacs" feature:
      http://dx.doi.org/10.1021/acs.jcim.6b00103
    o Updated TachyonL-OptiX GPU-accelerated ray tracing engine
      supports rendering of VR movies for YouTube with display
      by Google Cardboard, GearVR, Oculus Rift, etc:
      http://dx.doi.org/10.1016/j.parco.2015.10.015
      The new version also 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 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.

  Other updates and 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 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:
      http://dx.doi.org/10.1080/00268976.2013.813594
    o Built-in support for parallel analysis and visualization using
      MPI, with VMD "parallel" commands:
      http://dx.doi.org/10.1109/XSW.2013.10
      http://dx.doi.org/10.1109/HPTCDL.2014.7
    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:
      https://cug.org/proceedings/cug2 ... es/files/pap110.pdf
      http://www.ks.uiuc.edu/Publicati ... gi?tbcode=STON2016B
    o Updated support for compilation of VMD with Tcl 8.6.x

  New and improved plugins and extensions
    o Modified TkCon to prevent it from sourcing command line args
      as script files at startup.
    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 Bendix: calculates and visualizes both dynamic and static
      helix geometry, and abstracts helices without sacrificing conformation:
      http://sbcb.bioch.ox.ac.uk/Bendix/

  New and improved file import and export
    o pdbxplugin: support for the RCSB PDB "PDBx" format.
    o ccp4plugin: support for new IMOD tomography voxel formats

  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 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 other unusual structures.
    o fftk: misc small bug fixes.
    o Updated the VMD copy of WKFThreads from the latest version of Tachyon.