VMD User's Guide

• TachyonThe Tachyon multiprocessor ray tracing system and derivative code built into VMD is Copyright(c) 1994-2007 by John E. Stone. See the Tachyon distribution for redistribution andlicensing information.1.6 For information on our other softwareVMD is part of a suite of tools developed by the Theoretical and Computational Biophysics groupat the University of Illinois.• BioCoREBioCoRE is a web-based collaborative environment for structural biology which providestools to allow collaboration between researchers down the hall or around the world. Anyonewith access to the internet and a standard web browser can join BioCoRE and create or beadded to research projects, and information about a particular project is shared among allmembers of that project. More information is available at the BioCoRE home page 1• NAMDA parallel, object-oriented molecular dynamics code designed for high-performance simulationof large biomolecular systems. NAMD uses the CHARMM force field and file formatscompatible with both CHARMM and X-PLOR. NAMD supports both periodic and nonperiodicboundaries with efficient full electrostatics, multiple timestepping, constant pressureand temperature ensemble simulation methods. More information is available at the NAMDhome page 2• MDToolsMDTools is a collection of programs, scripts, and utilities provided for researchers to makevarious modeling and simulation tasks easier. More information is available at the MDToolshome page 3For more information on our software efforts, see the Theoretical and Computational BiophysicsGroup home page 4 .1 http://www.ks.uiuc.edu/Research/biocore2 http://www.ks.uiuc.edu/Researach/namd3 http://www.ks.uiuc.edu/Development/MDTools4 http://www.ks.uiuc.edu/13