VMD 1.8.7

Licence: Other Open Source
Version 1.8.7 | Release Date: 2009-08-01 | Download

What's new in VMD 1.8.7?
User documentation updates
o Minor improvements and corrections to the VMD User's Guide,
added documentation for new commands and environment variables.
o Added documentation for new volmap ligand options, "measure pbc2onc",
and "measure pbcneighbors"

Performance Improvements
o Added support for NVIDIA CUDA on MacOS X, both
32-bit and 64-bit Linux, and Windows.
VMD supports CUDA acceleration for electrostatics calculations
(for both direct summation "volmap coulomb" and
multilevel summation method "volmap coulombmsm"),
for implicit ligand sampling, and for
acceleration of molecular orbital display.
o Added support for multi-core processors to the
Windows versions of VMD and the included Tachyon ray tracer
o Tachyon's ambient occlusion lighting performance has been
significantly improved with respect to the number of
ambient occlusion samples taken. The new version operates
multiplicatively with the number of antialiasing samples, so that
if one uses 12 antialiasing samples, only about 8 to 16
ambient occlusion samples are needed for good shading results.

General Improvements
o New graphical interface controls for shadow rendering and
ambient occlusion lighting have been added to the
Display Settings menu. Currently, these only affect renderings
with TachyonInternal, or Tachyon.
o Updated the nucleic acid structure analysis and ribbon/cartoon
representations to handle the new PDB atom names "OP1" and "OP2",
which have replaced the older "O1P" and "O2P" atom naming convention.
o Color selection menus reorganized into subcategories

New representations and display features
o New "PaperChain" and "Twister" graphical representations for
display of carbohydrate structures in VMD
o New "Polyhedra" representation for display silicon nanodevice
o New "Orbital" representation displays and animates
molecular orbitals associated with the output of quantum chemistry
o New "outline" material property adds edge outlines on
drawn geometry. This material property is supported
with the GLSL interactive rendering mode, and for Tachyon renderings
o New ::vmd_pick_event callback for plugins to trace to get "pick" events
o PBC-aware trajectory smoothing

New and improved analysis commands
o General improvements of the plugin pbctools and a new function 'pbc
join' to join molecules that were broken due to wrapping over periodic
boundary conditions.
o new 'pbwithin' selection for selecting periodic neighbor atoms
within a cutoff distance
o new 'measure surface' command for finding surface atoms
o Added support for periodic boundary conditions to
the volmap implicit ligand sampling routines
o new 'measure pbc2onc' and 'measure pbcneighbors' commands.
o added three more demand-allocated per-timestep user-defined data fields
named "user2", "user3", and "user4",

Other features and improvements
o Added support for PowerPC based Linux for the Indiana 'BigRed'
Teragrid cluster
o Added support for Linux compilations using the Intel C/C++ compilers
o Secondary structure calculations using STRIDE are now able to
handle larger protein structures with up to 10,000 protein residues
and 100,000 atoms. Secondary structure calculations now propagate
error conditions if a STRIDE computation fails.
o Updated the py_numeric code for Python 2.5 and NumPy 1.x
o Updated the configure script to reference Python 2.5.x
o Greatly reduced the acceptable error tolerance for the RMS fitting
by default. The new tolerance is 1e-15, vs. the old tolerance which was
1e-5. The new code also accepts an environment variable
VMDFITRMSTOLERANCE which will override the default fit tolerance.
o Added support for an above/below stereo display mode for use with
special stereoscopic movie encoders
o Added recognition of SPC water.

New and improved plugins and extensions
o A new dynamic 'ruler' plugin for VMD for drawing ruled lines in 3-D
o New hydrogen bonds plugin for counting/plotting bonds over the course
of a molecular dynamics trajectory
o Updated the APBS plugin to allow dimension sizes n = a * 2^b + 1
for values of a other than 1.
o Updated vmdmovie plugin with correct transparency rendering flags
for movies made with Tachyon
o Updated the volmap plugin with support for the new
"Coulomb" potential map type

New and improved file import and export
o Updated bgfplugin with support for reading/writing
angles/dihedrals/impropers, and bug fixes.
o Updated ccp4plugin now reads and uses MRC2000 "ORIGIN" records
when available.
o Updated crdplugin now correctly reads trajectories that lack
line feeds between timesteps.
o Newly added dtrplugin reads Desmond trajectories, contributed
by D. E. Shaw Research.
o Improved compactness of ASCII-formatted DX files written by VMD
o Updated gamessplugin now reads wavefunction information, which can
be used to display molecular orbitals in VMD using the new
Orbitals representation.
o Updated lammpsplugin now supports newer style LAMMPS trajectories,
native LAMMPS text mode trajectories, adds support for many forms
of custom "dumps", and adds support for molecule ID, charges,
and velocities.
o Newly added maeffplugin reads structure files from
Schrodinger Inc's Maestro software, contributed by
D. E. Shaw Research.
o Updated mol2plugin with support for reading/writing
Antechamber bond orders, trajectories, and bug fixes.
o Updated msmsplugin to accept output from newer versions of MSMS
that emit comment lines at the top of the .vert and .face files.
o Updated parm7plugin to be more accepting of minor variations
in file structure so that VMD will read files written by other
AMBER-related software tools that don't strictly conform to the
output produced by the main AMBER tools.
o Updated pdbplugin now correctly clamps residue names to fit within
the fixed field width of the PDB format.
o Updated psfplugin to read and write angles/dihedrals/impropers and
cross-terms, for use by structure building tools.
o Updated situsplugin to add write support including the ability
to write orthogonal non-uniform cells by emitting a warning
and re-sampling the map on-the-fly.
o Updated version of vtfplugin by Olaf Lenz now supports loading and
saving more of the structure data in VMD.
o Updated xbgfplugin with support for reading/writing
angles/dihedrals/impropers, and bug fixes.

Bug Fixes
o Fixed a memory allocation bug with the 'within' distance selection
o Fixed Python callbacks
o Fixed memory leak in mol2plugin
o Fixed memory leaks in bgfplugin and xbgfplugin bond reading routines
o Fixed projection of surface normals into world coordinates
for isosurfaces of density maps with non-axis aligned basis vectors,
and/or opposite handedness coordinate systems.
o Fixed defaulted automatic color update behavior for coloring by
velocity, physical time, and user data per-timestep when
animating, or when using the draw multiple timesteps feature.

Version 1.8.6 | Release Date: 2009-03-17 | Download
No changes specified