This will allow the user to zoom in or out by moving the mouse horizontally while holding down the left mouse button. Go back to the Mouse menu and choose the Scale mode this time. It is now possible to move the molecule around when you hold the left mouse button down.Ĩ. Choose the Translation mode and go back to the OpenGL Display. Mouse modes and their characteristic cursors.ħ. Topics covered in this tutorial include visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins. It is impossible to cover all of VMD’s capabilities in one unit instead we will present several step-by-step examples of VMD’s basic features. This unit will serve as an introductory VMD tutorial. Interactive molecular dynamics simulationsĮxtensions to the Tcl/Python scripting languagesĮxtensible source code written in C and C++ Rendering high-resolution, publication-quality molecule imagesīuilding and preparing systems for molecular dynamics simulations No limits on the number of atoms, molecules, or trajectory frames, except available memory Support for most molecular data file formats General 3-D molecular visualization with extensive drawing and coloring methodsĮxtensive atom selection syntax for choosing subsets of atoms for display Among molecular graphics programs, VMD is unique in its ability to efficiently operate on multi-gigabyte molecular dynamics trajectories, its interoperability with a large number of molecular dynamics simulation packages, and its integration of structure and sequence information. It is developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. VMD (Visual Molecular Dynamics) ( Humphrey et al., 1996) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc.
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