VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Mac OS X, UNIX, or Windows, is distributed free of charge, and includes source code.

New Features and Performance Improvements

• Fast GPU-accelerated quality-of-fit cross correlation enables analysis of results from molecular dynamics flexible fitting (MDFF) and other hybrid structure determination methods
• New built-in TachyonL-OptiX GPU-accelerated ray tracing engine speeds up high quality image and movie renderings, particularly for scenes using ambient occlusion lighting and shadows
• VMD now 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
• Built-in support for parallel analysis and visualization using MPI, with new VMD "parallel" commands
• Added initial support for large scale parallel scripting with Swift/T
• VMD supports off-screen OpenGL rendering, enabling large scale parallel visualization runs on "headless" GPU clusters and petascale computers, using a new "-dispdev openglpbuffer" flag
• An improved "QuickSurf" molecular surface representation allows molecular dynamics trajectories to be animated for selections of 10,000 to over 1,000,000 atoms depending on the speed of the host machine. Fast multi-core and GPU-accelerated implementations of the QuickSurf representation enable faster/smoother trajectory playback for moderate system sizes, and interactive surface calculation for systems containing up to 100 million atoms on machines with sufficient host and GPU memory capacity
• The improved QuickSurf implementation now supports visualization of coarse-grained and cellular scale models

Other updates and improvements

• Added initial support for ARM processors and the Android OS
• Added support for compilation of VMD with Tcl 8.6.x

New and improved plugins and extensions

• Bendix: calculates and visualizes both dynamic and static helix geometry, and abstracts helices without sacrificing conformation
• 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
• MDFF: added option in mdff setup to use implicit solvent
• NetworkView: a plugin for the study of allostery and signalling through network models, allowing networks can be loaded and mapped onto molecular structures loaded in VMD
• NMWiz: A normal mode analysis plugin
• psfgen: Add non-plugin NAMD binary file writing command "writenamdbin". Properly handle insertion codes by appending the code to the resid string as in "48A". Read and write insertion code in resid field of psf file. Add "readpsf file.psf pdb file.pdb" to read insertion code from pdb file. Add "regenerate resids" to remove insertion codes with minimal residue renumbering. Leave atoms in reasonable order when applying patches. Do not generate O-H-H angles (assume these are water molecules). Free old memory when regenerating angles or dihedrals for entire structure. Handle masses as large as 99999. Use 6-wide atom type when writing CHARMM EXT format X-PLOR psf file. Use field width of 10 when reading CHARMM EXT angles/dihedrals/impropers/cmaps.
• Remote: A plugin for managing VMD remote control connections from mobile phones and wireless tablet devices
• Timeline: improved graphical interface with better zooming, and improved display of very long timescale trajectories
• topotools: New topogromacs features, allow support replication of non-orthogonal cells, handle low-dimensional system box dimensions consistent with LAMMPS, fix bug in writing non-orthogonal boxes reported by Sandeep Kumar Reddy, add support for new Coeff section in LAMMPS data files, add support for writing LAMMPS data files with triclinic cells.
• Modified TkCon to prevent it from sourcing command line args as script files at startup.

New and improved file import and export

• cubeplugin: Make the parser for the cubefile header more resilient when new fields are added like in g09 rev d.01.
• dcdplugin: Changed the dcdplugin reader code to avoid using readv() to prevent problems when reading 240M-atom trajectories on some versions of Linux.
• dlpolyplugin: Fixed a typo in the PBC unit cell basis vector orthogonality check.
• gamessplugin: Fixed reading of minimization steps for recent builds of Firefly 8
• gromacsplugin: Updates to gromacsplugin adding .gro write support, contributed by Magnus Lundborg. Changed .gro parsing code to use fixed field widths to address problems with files that had no spaces between the coordinate fields.
• jslugin: Changed the jsplugin reader code to avoid using readv() to prevent problems when reading 240M-atom trajectories on some versions of Linux.
• lammpsplugin: Support LAMMPS native trajectories with variable number of atoms through provisioning constant storage via an environment variable LAMMPSMAXATOM. Fixed bug in handling triclinic cells with negative tilt factors.
• maeffplugin: Fixed uninitialized optflags state in maeffplugin, so that compilations that don't define DESRES_CTNUMBER will behave correctly.
• moldenplugin: Fixed various limitations that had previously caused problems for Terachem users. Use case-insensitive string comparisons when reading shell types from Molden files.
• molemeshplugin: Added Brian Bennion's plugin for reading mesh files produced by MOLE 2.0.
• offplugin: Fixed internal initialization bug
• psfplugin: Handle various bond/angle/dihedral/improper misformattings for 10M-100M-atom structures. Made the PSF plugin allow NAMD-tagged PSF files to use a space delimited bond record format since NAMD accepts that variation.
• rst7plugin: Added support for reading and writing box and velocity information.
• tngplugin: Added support for the new Gromacs TNG plugin
• vtfplugin: Allow compilation of VTF plugin without Tcl, updated to latest version by Olaf Lenz
• xsfplugin: Fixed a problem with the interpretation of the cell vectors in cases that must be rotated.

User documentation updates

• Minor improvements and corrections to the VMD User's Guide, added documentation for new commands, graphical representations, and environment variables.
• parsefep: Updated ParseFEP docs with latest files from Chris Chipot.
• vdna: Updated Tom Bishop's contact info in the docs

Bug fixes and small improvements

• NetworkView: small GUI improvements and fixes
• fftk: fixes to GenZMatrix to allow for more general ACC/DON assignments
• Fixed a potential crash in the x86 SSE-accelerated version of the wavefunction calculation for the Orbital representation
• Fixed an Interactive MD force cancellation bug that occured most frequently when using Mouse-based control and multi-atom targets
• Fixed an old bug with 2-atom and 3-atom alignments
• Fixed a bug prevented clean compilations without Tcl, needed for early Android testing.
• Updated the VMD copy of WKFThreads from the latest version of Tachyon.