README file for VMD 1.6.1 --------------------------------------------------------------------------- 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 Stereoscopic display capability using Red/Blue or LCD shutter glasses. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). 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 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 Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl and Python languages 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 information: http://www.ks.uiuc.edu/Research/namd o VMD can be used to interactively display and control an MD simulation using NAMD or Protomol. o Integration with the BioCoRE collaborative research environment. VMD can "publish" molecular graphics scripts to BioCoRE, so that BioCoRE collaborators can work together over the internet. See the BioCoRE WWW home page for more information: http://www.ks.uiuc.edu/Research/biocore What's new in VMD 1.6.1? ------------------------ New Features o Some builds of VMD now support multiprocessor acceleration and multithreading for improved I/O performance even on uniprocessors. o Multithreaded IMD socket I/O for improved performance on high latency networks and with slow simulations. o Ported VMD to MacOS-X using Mesa, requires XFree86 be installed. o Support for 64-bit versions of VMD on IRIX 6.x and Solaris 2.x, using R10000 class SGI CPUs, and UltraSPARC class Sun CPUs. The 64-bit versions are capable of working with files larger than 2GB, and can use more than 4GB of main memory if necessary. o New "getbonds" and "setbonds" commands for Tcl and Python atom selections. Replaces older "bond" command. o New real-time implementation of anaglyph (red/blue) stereo for people without LCD glasses, but with quad-buffered stereo hardware on their machine. o New atom selection keyword 'exwithin', eliminates need for a commonly used complex combination of atom selections '(within 3 of X) and not X'. o Works with BioCoRE. VMD can now "publish" configuration files to a BioCoRE notebook, such that collaborators can work together on VMD visualizations, using BioCoRE as their common workplace. General Improvements and Bug Fixes o Tcl "atomselect get" speed increased by 10-30x for large molecules for numeric selections. String-based selections slightly slower, but a good improvement for the common performance intensive use-cases. o Increased speed of "lines" representation drawing and animation by a factor of 3, allowing interactive rotation of huge systems in lines mode (4 million atom water box at 2 seconds per frame.) o Significant improvements in responsiveness in the the graphics form "atom name lists" for large molecules with hundreds of thousands of atoms. Very large name lists now display 10 to 30 times faster. o Increased the number of colors in the color scale map from 16 to 1024. o Significant updates to Python callback mechanism. o Fixed a minor EOF failure in G96 file reader o Built with FLTK 1.0.10 on all platforms. o Fixed PRs (bugs): 134, 136, 139, 140, 141, 145, 146, 148, 150, 151, 152, 153 User Interface Changes o The rmsd fit routines can be brought up without needing to source a fully qualified pathname in the VMD installation directory o Updated the "Sim" form to improve the IMD interface User Documentation Updates o Updated interactive molecular dynamics (IMD) features for the current implementation o Documentation for new anaglyph stereo feature o Documented new RMSD fit startup feature 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 --------------------- BioCoRE, JMV, MDTools, NAMD, VMD and the Structural Biology Software Database represent the broad 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/biocore/ http://www.ks.uiuc.edu/Research/NAMD/ http://www.ks.uiuc.edu/Research/VMD/ http://www.ks.uiuc.edu/Development/biosoftdb/ http://www.ks.uiuc.edu/Development/JMV/ http://www.ks.uiuc.edu/Development/MDTools/ The VMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969). Disclaimer and Copyright ------------------------ VMD is Copyright (c) 1995-2001 the Board of Trustees of the University of Illinois and others. 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. 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 VMD manuals are available which describe how to install, use, and modify VMD. The VMD installation guide, is contained in the VMD distribution in the file "doc/ig.ps". The User's Guide and Programmer's Guide are available separately (due to size) from the VMD web site. Quick help may be accessed by pressing the "Help" button on the main VMD form, or by typing help in the VMD command window. This will bring up the VMD quick help page, and will lead you to several other VMD help files and manuals. Quick Installation Instructions ------------------------------- The Windows version of VMD is distributed as a self-extracting archive, and should be entirely self explanatory. Detailed instructions for compiling this version of VMD can be found in the installation guide. 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: http://www.ks.uiuc.edu/ VMD: http://www.ks.uiuc.edu/Research/vmd/ README for VMD; last modified April 22, 2001 by John Stone