.. -*- coding: utf-8 -*- Visualizing and analysing Molecular Dynamics trajectories with VMD ================================================================== .. Note:: Short URL for this page: https://goo.gl/QD1BKx This tutorial provides a short introduction to basic use of the VMD_ ("Visual Molecular Dynamics") software to visualize and analyze molecular dynamics (MD) trajectories. It is part of the ASU_ course `PHY 542/NAN 542 — Topics in Biophysics I`_. For a quick introduction on using VMD_ look at `Protein visualization and analysis with VMD`_. We will use data from [Beckstein2009]_ as well as an unpublished trajectory. Basics of MD simulations can be found in [FrenkelSmit]_, [Mura2014]_ and in the lecture notes. Contents ======== We are going to work through the individual sections in order. Use the navigation links in menu bar to move forward and backwards. .. toctree:: :maxdepth: 1 dynamics/index movies Learning Objectives =================== - loading of dynamics trajectories - viewing a trajectory - use of RMSFitting tools - analysis of dynamic collective variables References ========== .. _VMD: http://www.ks.uiuc.edu/Research/vmd .. _1AKE: http://dx.doi.org/10.2210/pdb1ake/pdb .. _ASU: http://asu.edu .. _`PHY 542/NAN 542 — Topics in Biophysics I`: https://becksteinlab.physics.asu.edu/learning/40/phy542-nan542-phy498-topics-in-biophysics-i .. _`Protein visualization and analysis with VMD`: https://becksteinlab.physics.asu.edu/pages/courses/2016/PHY542/practicals/vmd/ .. [FrenkelSmit] D. Frenkel and B. Smit. Understanding Molecular Simulations. Academic Press, San Diego, 2002. .. [Mura2014] C. Mura and C. E. McAnany. An introduction to biomolecular simulations and docking. Molecular Simulation, 40 (2014), 732–764. doi:`10.1080/08927022.2014.935372 `_ .. [Beckstein2009] O Beckstein. EJ Denning, JR Perilla, and TB Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open/Closed Transitions. J Mol Biol 394 (2009), 160--176. doi:`10.1016/j.jmb.2009.09.009 `_ Indices and tables ================== * :ref:`genindex` * :ref:`search`