ソフトウェア

名称： VMD
最新バージョン：1.9.3

リリースノート：
https://www.ks.uiuc.edu/Research/vmd/current/README.html

What’s new in VMD 1.9.3?
————————
New platform support:
o Added support for Cray XC50 supercomputers with NVIDIA 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:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/avx512.html
o Support for IBM POWER8 CPUs and the new “Minsky” compute node
that incorporates NVIDIA P100 GPUs attached via NVLink,
for the upcoming ORNL CAAR early access system:
http://dx.doi.org/10.1007/978-3-319-46079-6_14
o Support for a range of ARM processors paired with GPUs:
http://dx.doi.org/10.1109/IPDPSW.2016.130

New Features and Performance Improvements
o New QwikMD integrative MD simulation tool guides users in
preparing, running, and analyzing MD simulations:
http://dx.doi.org/10.1038/srep26536
http://www.ks.uiuc.edu/Research/qwikmd/
o Automated Topology Conversion from CHARMM to GROMACS with
the topotools plugin “topogromacs” feature:
http://dx.doi.org/10.1021/acs.jcim.6b00103
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.
http://dx.doi.org/10.1109/TVCG.2016.2599041
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:
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
http://dx.doi.org/10.1109/IPDPSW.2016.121
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/cug2014_proceedings/includes/files/pap110.pdf
http://dx.doi.org/10.1109/IPDPSW.2016.127

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:
http://dx.doi.org/10.1039/C4FD00005F
http://dx.doi.org/10.1007/978-3-319-46079-6_14
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 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/
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.