VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 18 2011 - 11:54:35 CST

Hi,
  Thanks for the feedback.
On linux I'm fairly confident that things should be working well,
but we're looking for things like the bug the cropped up the other day
where some files were missing from one of the plugins. So I'd suggest
that testing the various plugins would be most helpful at this moment.

On Windows and Mac I'm interested in a broader range of feedback,
particularly including the behavior of the GUI and the installers too.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 18, 2011 at 12:19:38PM -0500, Joseph Bylund wrote:
> Build went well on "Linux 2.6.35-25-generic #44-Ubuntu SMP x86_64
> GNU/Linux" and it seems to be running smoothly. Is there anything in
> specific you want us to test? Thanks for the great program.
> -Joe
>
> On 02/16/2011 12:21 PM, John Stone wrote:
> >Dear VMD-L,
> > Here is a preliminary list of the new features and improvements
> >in the VMD 1.9 beta release I posted yesterday:
> >
> >What's new in VMD 1.9?
> >----------------------
> > User documentation updates
> > o Minor improvements and corrections to the VMD User's Guide,
> > added documentation for new commands and environment variables.
> >
> > Performance Improvements
> > o The "Orbital" representation can now utilize multiple GPUs to
> > greatly accelerate rendering.
> > o New CUDA-based multi-GPU radial distribution function calculation,
> > with the "measure rdf" command.
> > o Added initial support for OpenCL accelerated molecular orbital
> > rendering.
> > o Added initial support for OpenCL accelerated electrostatic potential
> > calculations for "volmap coulomb".
> >
> > General Improvements
> > o Added "tooltip" mouse-over help and tips to all of the VMD
> > graphical user interface controls.
> > o Global label properties are now located in a new tab within
> > the labels window.
> >
> > New rendering and display features
> > o Updated default representation resolutions for modern era GPUs,
> > depth cueing is now enabled by default on platforms that support it.
> > o New and updated stereoscopic display support:
> > The left and right eyes can now be swapped in any stereo mode,
> > so the old "Reverse" mode names have now been eliminated.
> > Anaglyph stereo no longer requires a GPU with support for
> > quad-buffered stereo.
> > Added support for column-interleaved and checkerboard stereo modes.
> > Reorganized stereo controls in the VMD display menu.
> > o The "display resize" and "display reposition" commands are now
> > implemented on all platforms.
> > o Added a new angle-modulated transparency material property that
> > works similarly to the way Raster3D renders transparent surfaces.
> > The angle-modulated material property is supported in the
> > VMD OpenGL Window, and in Raster3D and Tachyon renderings.
> > o Added new "thickness" controls for atom label text and for
> > user-defined text drawn using the "graphics" or "draw" commands.
> > Added code to draw points at font stroke vector endpoints, to
> > prevent "cracks" from appearing when larger line widths are used.
> > o VMD atom labels and text are now exported to renderings by
> > Gelato, Raster3D, POV-Ray, RenderMan, and Tachyon.
> > o The format of VMD scenes exported to the RenderMan .RIB format
> > has been updated for the latest versions of PIXAR Photorealistic
> > RenderMan, and have also been tested with Aqsis, an open source
> > RenderMan compatible renderer.
> > o Tachyon renderings now support gradient backgrounds, and have been
> > updated to more faithfully implement all of the VMD depth cueing
> > modes.
> > o Added export of representation group hiearchy and
> > material properties to Wavefront OBJ files. Wavefront .OBJ files
> > generated by VMD now take advantage of a more efficient triangle
> > mesh
> > storage format that reduces file sizes to half their original size.
> > Corrected the polygon winding order for spheres and cylinders,
> > needed for correct two-sided lighting in Maya.
> > o Increased interactive molecular dynamics force arrow scaling
> > constant by a factor of 3.
> >
> > New and improved analysis commands
> > o New "measure rdf" command provides fast GPU-accelerated
> > calculation of radial distribution functions.
> > o The "volmap coulombmsm" command now supports both periodic
> > and non-periodic simulation cells (both are also GPU-accelerated).
> > o New "parallel" commands enable MPI-based compilations of VMD to
> > perform batch mode parallel analysis jobs on distributed memory
> > clusters and supercomputers. The "parallel" commands also exist
> > within non-MPI versions of VMD, so that any analysis script can
> > be written to automatically adapt to parallel execution.
> > Parallel collective operations (allgather, allreduce, barrier)
> > make it possible for parallel analysis jobs to process results
> > without
> > using hand-written message passing code and without exchanging data
> > through the filesystem.
> >
> > Other features and improvements
> > o Enable a much broader range of keycodes in the OpenGL graphics
> > window,
> > allowing VMD user-defined hotkeys to be associated with the
> > 12 function keys, keypad arrows, page-up/down, home, end, insert,
> > and delete.
> > o Enable mirror specular reflections for Tachyon renderings when
> > the environment variable VMDTACHYONMIRRORSPECULAR is set.
> > Implemented a user-definable threshold for enabling mirror
> > reflection
> > in Tachyon renderings when the Phong exponent goes beyond a
> > specified
> > limit. The VMDTACHYONPHONGSPECTHRESH variable can be set to
> > choose a different threshold for enabling mirror reflection.
> > o Added VMDCUDADEVICEMASK environment variable to give the user
> > explicit control over the subset of GPUs that VMD is allowed to use.
> > o Added VMDNOCUDA environment variable to allow the user to prevent
> > VMD from using GPUs for non-rendering purposes.
> > o If .vmdsensors file VRPN device names contains @tcp, we enforce
> > tcp-only connections which can be easily punched through firewalls
> > and tunneled with ssh.
> > o Changed the default behavior of X-Windows based VMD builds to
> > automatically run VMD in text mode if the DISPLAY environment
> > variable is unset.
> > o Updated VMD to support Tcl 8.6 API changes.
> > o Updated VMD to support FLTK 1.1.10
> > o Updated VMD to support CUDA 3.x, and 4.0
> >
> > New and improved plugins and extensions
> > o autoimd: Added support for the new chirality and cispeptide plugins.
> > o autoionize: Added ion placement modes to neutralize the system or
> > set
> > a salt concentration. Added support for all ions in the CHARMM force
> > field. Automatically set segname of ions to be placed to avoid
> > duplicated segments.
> > o autopsf: correcting the behaviour of "reset autopsf".
> > o chirality: New plugin for identifying, visualizing, fixing, and
> > preventing chirality errors in molecular dynamics simulations.
> > o cispeptide: New plugin for identifying, visualizing, fixing, and
> > preventing cis peptide bonds in molecular dynamics simulations.
> > o clonerep: bug fix enabling use of atom selections containing
> > perl regular expressions.
> > o colorscalebar: Maintains current views of all molecules when the
> > scale
> > bar is added. New GUI option to select molecule and representation
> > to
> > use with the autoscale option.
> > o hbonds: added warning about overlapping selections in measure
> > hbonds.
> > o idatm: modified molefacure and runante to be able to run geometry
> > optimisations using sqm.
> > o ilstools: Bug fix for package require ordering problem pointed
> > out by Aaron Oakley.
> > o mdffplugin: New plugin that implements the Molecular Dynamics
> > Flexible
> > Fitting (MDFF) simulation preparation and analysis tools for docking
> > all-atom structures with Cryo-EM density maps.
> > o membrane: added the option to build CHARMM36 bilayers.
> > o molefacture: Update molefacture to use the new ambertools version
> > of antechamber.
> > o multiseq: Support for the multiple sequence alignment tool MAFFT
> > which offers fast multiple alignment methods and can be used
> > anywhere
> > within MultiSeq that clustalw is used. The desired title shown
> > for a sequence can now be changed from simply 'Sequence Name'
> > to a variety of options including Scientific Name, Common Name,
> > Domain of Life, and many others.
> > RMSD and Q calculations work for RNA as well as DNA.
> > Numerous memory footprint reductions and speed improvements
> > particularly beneficial for loading large numbers (e.g. 100,000)
> > of sequences. Lines can now be chosen as a rep type for a given
> > sequence or for highlighting. MultiSeq can load dot-bracket
> > notation files for a given sequence and they can be viewed
> > in the main window.
> > o namdgui: Fixed menubutton behavior for MacOS X.
> > o nanotube: Automatically assign bond types and make certain
> > that bonds are written out. Now uses topotools plugin
> > instead of writing temporary files. Bug fixes and strict
> > parameter checking.
> > o pbctools: New compound options for 'pbc join': fragment, connected.
> > Alternate joining algorithm based on bondlists. slower, but
> > can handle arbitrarily long molecules. The 'pbc box' command
> > now allows the drawing material to be set. Several bug fixes.
> > o qmtool: Fixed menubutton behavior for MacOS X.
> > o readcharmmtop: New CHARMM topology for lipids.
> > o readcharmmpar: New CHARMM topology for lipids.
> > o rnaview: Now ships with external program RNAView that calculates
> > base
> > pairing information from nucleic acid structures (used by the
> > ssrestraints plugin).
> > o runante: Scale CM1 charges by 1.14 (Jorgensen's recommendation)
> > o solvate: Fixed a bug that could lead to incomplete overage of the
> > solute.
> > o ssrestraints: Fixed parsing of -hbonds option. Added support for
> > Amber
> > RNA residue names.
> > o symmetrytool: Fixed menubutton behavior for MacOS X.
> > o timeline: Handles large structures much more efficiently.
> > o topotools: many bugfixes from version 1.0. Determination of angle,
> > dihedral and (some) improper definitions (with adjustable tolerance)
> > from bond topology data. Heuristic determination of atom
> > properties based on other information (e.g. element from mass,
> > mass from element, element from name, radius from element, etc).
> > Support for reading and writing of xmol/xyz style trajectories with
> > a
> > varying number of atoms (when bonds are not displayed).
> > Support for writing synthetic gromacs topology files for
> > use with gromacs analysis tools for non-gromacs trajectories.
> > Support for reading data files containing non-orthogonal cells.
> > Stricter checking for CGCMM extensions to the LAMMPS data file
> > format.
> > Encode the intended atom_style setting in data file header.
> > Parse and compare - if present - against requested atom style on
> > reading. - write commented out Coeff sections to data files to
> > provide hints on which coefficients need to be set.
> > o vdna: Updated with Tom Bishop's latest version.
> > Fixed uninitialized data preventing the "plot parameters" button
> > from being used before drawing the DNA.
> > o viewmaster: Updated handling of material properties for new
> > features.
> > o vmdmovie: Added support for both MPEG-1 and MPEG-2 formats using
> > mencoder. Added support for current ffmpeg 0.5.x encoder on Unix
> > platforms. Added 4 new FFMPEG encoding targets including MPEG-1,
> > MPEG-2, and both NTSC and PAL forms of MPEG-2 DVD profiles.
> > Fixed ppmtompeg frame counters to handle movie sequences with
> > up to 100000 frames.
> > o volutil: New plugin for processing Cryo-EM volumetric density map
> > files,
> > used by the MDFF plugin.
> >
> > New and improved file import and export
> > o Abinit plugin: Added Rob Lahaye's VMD plugin for reading ABINIT
> > files.
> > o CHARMM COR plugin: prevent uninitialized variables on some
> > platforms.
> > o DCD plugin: Detect and works around bugs in DCD files written by
> > older versions of Vega ZZ which generated incorrectly formatted
> > DCD trajectories.
> > o DTR plugin: Misc bug fixes provided by DESRES.
> > o HOOMD plugin: Added support for new acceleration field.
> > o LAMMPS plugin: allow remapping of fields via an environment
> > variable.
> > Added read support for triclinic simulation cells.
> > Improved precision of PBC box angle computation.
> > Improved support for reading of atoms sorted by their atom id.
> > Added support for writing trajectory files of non-orthogonal cells.
> > o MAEFF plugin: Latest version of Maestro plugin from DESRES.
> > This version adds support for Smiles strings.
> > o MDF plugin: handle MDF files containing more than 9 molecules, catch
> > and gracefully handle any problems with bond parsing.
> > o Molden plugin: Fixed memory leak, and improved documentation.
> > Enable splitting SP-shells into one S- and one P-shell.
> > o PSF plugin: Added preliminary parsing of CHARMM PSF files
> > constructed
> > for the Drude polarizable forcefield. Gracefully handle PSF files
> > that contain missing or incorrect bond information.
> > o PQR plugin: now handles HETATM records correctly, and gracefully
> > handles
> > some varations in file structure
> >
> > Bug Fixes
> > o The Python global interpreter lock (GIL) is held when callbacks
> > are invoked to prevent problems with Tk events come in.
> > o Fixed incorrect material property tags for Python materials
> > interface.
> > o Fixed a potential memory corruption problem in "within" selections
> > on systems with fewer atoms than CPU cores.
> > o Fixed the polygon winding order for two-radius cones for polygonal
> > renderers.
> > o Updated atom picking logic to take into account clipping of
> > displayed geometry (and thus associated pick points) against both
> > the view frustum and the active set of user-defined clipping planes.
> > o Fixed a case where wireframe Surf renderings were
> > leaving the linestyle and line width unspecified.
> > o Catch NULL pointers, which can (very rarely) be returned by
> > OpenGL drivers if certain types of catastrophic errors occur.
> > o Fix memory leak when defining angles, dihedrals and impropers via '
> > molinfo set angles'.
> > o Excluded old Cygwin-based builds of the "intersurf" plugin
> > that encounter problems with recent Cygwin installations.
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078