标题: VMD 1.9.3 beta1 Released! [打印本页] 作者Author: greatzdk 时间: 2016-8-16 14:11 标题: VMD 1.9.3 beta1 Released! 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.