README file for VMD 1.4 --------------------------------------------------------------------------- What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/ --------------------------------------------------------------------- VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. The program has many features, which include: o No limit on the number of molecules, atoms, residues or number of animation frames, except available memory. o Many molecular rendering and coloring methods. o Stereo display capability. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Radiance, Raster3D, Rayshade, and Tachyon. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis. o Modular, extensible source code using an object-oriented design in C++, with a programmer's guide outlining the source code structure. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: http://www.ks.uiuc.edu/Research/namd VMD can be used to interactively display and control an MD simulation using NAMD. What's new in VMD 1.4? ---------------------- Platform Support o Full support for Microsoft Windows 95/98/NT with hardware accelerated OpenGL based 3-D rendering. New Features o Support for reading Gromos96 trajectories (ASCII-only). o Completely rewritten 3-D Tracker support which supports haptic force feedback, improved tools, and new user interface elements. o Completely redesigned interactive molecular dynamics support code, which replaces the older MDComm code. The new code works on all supported Unix platforms, and is built into VMD by default since it is very small and efficient. o Completely new font rendering code, which is more flexible, and supports new sizing capabilities. o New DCD file reader automatically performs byte-swapping when reading little-endian files on a big-endian machine, and vice versa. o Completely rewritten regular expression handling system. VMD now uses PERL style regular expressions, and is much more efficient. o The OpenGL versions of VMD now implement a fast "screen-door" transparency algorithm which provides a basic transparency feature with no degradation to overall VMD rendering performance. Publication quality rendering of transparency effects still requires the use of external ray tracing software. o New backface culling feature helps improve rendering performance on low-end machines with minimalistic graphics hardware. General Improvements and Bug Fixes o Greatly reduced CPU time consumption when idle (not rotating etc..) VMD keeps track of the exact circumstances that require a display redraw, and only runs the graphics hardware when necessary, rather than continously as previous versions did. o Improvements in several internal data structures, resulting in increases in molecule loading speed for large files. Tests with a 206,750 atom system yielded a 20-fold increase in speed over previous versions of VMD. o The "within" distance-based atom selections now run 50 to 100 times faster through the use of a grid-based spatial decomposition. o The "same residue as" atom selections now run 50 to 100 times faster through the use of a hash-table-based binned acceleration data structure.. o Improved the depth cueing code in VMD, so that it works much better on all platforms. The depth cueing effect is much more pronounced, and is no longer affected by bugs in old graphics accelerator implementations. o The Radiance, Raster3D, and Tachyon scene exports have been improved substantially over previous versions of VMD, and now support current versions of these packages. o The PostScript renderer feature now runs much faster, generates smaller files, and supports more primitives than previous versions. Several bugs in memory deallocation have also been fixed. o Updated the VMD code that implements "mol pdbload" for direct loading of proteins from the RCSB, using their new database layout. o Fixes to OpenGL Display Device code for window position and size. o Improved overall efficiency of many parts of VMD, and cleaned up several of its basic classes/templates. o Extensive audit of VMD 1.4 documentation, including rewritten chapters for interactive molecular dynamics simulations, and VMD 3-D tracker support. o Mesa versions of VMD are now built using Mesa 3.1 o VMD no longer depends on the GNU libg++ string classes, it uses its own string class, which is much smaller and more efficient for the tasks VMD uses it for. This also simplifies the VMD compilation process substantially. User Interface Changes o Several of the "popup" menu interfaces in VMD have been eliminated in favor of the portable "Form" based interfaces. o New "tool selection" button in the graphics form. o New "culling" button in the display form. o Completely redesigned Tracker form. o Redesigned Sim form. User Documentation Updates o New Windows platform notes in the VMD installation guide o Updated sections in the User guide pertaining to interactive molecular dynamics with NAMD, and the use of spatial trackers and haptic feedback devices with VMD. Known bugs ---------- Please visit the VMD web site for information on known bugs, workarounds, and fixes: http://www.ks.uiuc.edu/Research/vmd/ Cost and Availability --------------------- VMD, NAMD, and BioCoRE represent the broad range efforts of the Theoretical Biophysics group, an NIH Resource for Macromolecular Modeling and Bioinformatics, designed to develop and distribute free, effective tools (with source code) for molecular dynamics studies in structural biology. For more information, see: http://www.ks.uiuc.edu/Research/VMD/ http://www.ks.uiuc.edu/Research/NAMD/ http://www.ks.uiuc.edu/Research/collaboratory/ The VMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969). Disclaimer and Copyright ------------------------ VMD is Copyright (c) 1995-2000 the Board of Trustees of the University of Illinois and others. Portions of VMD code are Copyright (c) 1997-1998 Andrew Dalke The terms for using, copying, modifying, and distributing VMD are specified in the file LICENSE. If you use VMD in a way you think is interesting or novel, we would like to know about it. Please take a few minutes to fill out a registration form at http://www.ks.uiuc.edu/Research/vmd/VMDregistration.html if you are going to use VMD. The authors request that any published work which utilizes VMD includes a reference to the VMD web page: http://www.ks.uiuc.edu/Research/vmd/ and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. Documentation ------------- Three postscript documentation files are available for VMD which describe how to install, use, and modify VMD. One, the installation guide, is contained in the VMD distribution in the file doc/ig.ps . The other two, the User's Guide and Programmer's Guide are available separately (due to size) from the VMD web site. A quick help file in HTML format, 'vmd_help.html' is also available, in the 'data' directory of the distribution. This file may be viewed by any HTML viewer, and is used to provide on-line help for VMD when it is running. For the latest information on VMD, please see the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ This page contains links to HTML versions of all three VMD manuals listed above, and info on the latest release of the program. A brief VMD FAQ is also available, and can be found either by looking at the VMD home page, or directly via the URL: http://www.ks.uiuc.edu/Research/vmd/vmd_faq.html Installation ------------ Detailed instructions for compiling this version of VMD can be found in the installation guide, ig.ps. For quick installation of the binary distribution for Unix do the following: 1) uncompress and untar the distribution into a working directory. In this working directory, there are several subdirectories such as bin, src, doc, data, as well as this README and a configure script. Change to this working directory after the unpacking is complete. 2) Edit the file 'configure'; change the values for the $install_library_dir and $install_bin_dir to a directory in which vmd data files and executables should be installed: $install_bin_dir is the location of the startup script 'vmd'. It should be located in the path of users interested in running VMD. $install_library_dir is the location of all other VMD files. This included the binary and helper scripts. It should not be in the path. 3) A Makefile must be generated based on these configuration variables by running "./configure". 4) After configuration is complete, cd to the src directory, and type "make install". This will install VMD in the two directories listed above. Note that running "make install" twice will print error messages because you are attempting to overwrite some read-only files. This should be fine. 5) When installed, type 'vmd' to start (make sure the $install_bin_dir directory is in your path). Required Libraries ------------------ VMD requires several libraries and programs for various of its functions. In particular, it uses GL or OpenGL based 3-D rendering, and will require that you have the appropriate GL or OpenGL libraries on your system. Other programs are required by some of VMD's optional features. Please visit the VMD web site for more information: http://www.ks.uiuc.edu/Research/vmd/ For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'. VMD Development Team Theoretical Biophysics Group University of Illinois and Beckman Institute 405 N. Matthews Urbana, IL 61801 TBG WWW: http://www.ks.uiuc.edu/ VMD WWW: http://www.ks.uiuc.edu/Research/vmd/ README for VMD; last modified January 7, 2000 by John Stone