#VMD TUTORIAL HOW TO#
#VMD TUTORIAL MOVIE#
#VMD TUTORIAL PDF#

Work through the вЂњWorking with Still FramesвЂќ section, and the вЂњBasicвЂќ section of вЂњWorking with TrajectoriesвЂќ.

The knowledge of the material in this tutorial is not required to complete (most of) the Gromacs exercises.

#VMD TUTORIAL PDF#

The tutorial can be found here: imgmv-tutorial.html The files required for the tutorial are also available on the machines in the course folder under VMD-Images-and-Movies/imgmv-tutorial-files/, and a PDF version of the tutorial in VMD-Images-and-Movies/imgmv-tutorial.pdf. VMD Images and Movies Tutorial If you already have some experience on VMD, you may find the VMD Images and Movies Tutorial useful to learn more about advanced visualization options available through the GUI. The вЂњScripting in VMDвЂќ section provides a basic introduction to the scripting capabilities of VMD, which we will discuss more in the afternoon.

#VMD TUTORIAL MOVIE#

The Gromacs exercises assume that you are on some level familiar with the contents of the sections вЂњWorking with a Single MoleculeвЂќ, вЂњTrajectories and Movie MakingвЂќ, and вЂњWorking with Multiple MoleculesвЂќ of the tutorial. html The files required for the tutorial are also available on the machines in the course folder under VMD-Tutorial/vmd-tutorial-files/, and a PDF version of the tutorial in VMD-Tutorial/vmd-tutorial.pdf. VMD Tutorial If you have little or no previous experience of VMD, a great place to start is to work through the official VMD Tutorial. They rely heavily on tutorial material available from the official VMD site. Introduction to VMD With these exercises, you can familiarize yourself with the graphical user interface of VMD and different kinds of visualizations that you can create.

#VMD TUTORIAL HOW TO#

VMD Hands-On Exercises: Basics Before lunch In the morning session, the exercises are divided into two groups: 1) working through VMD tutorials to get to know VMD for those that are not very experienced in using the VMD graphical user interface (some of the tutorial material is also useful for users that already have a significant amount of experience on VMD), and 2) Gromacs-specific sections for those who know the basics of using VMD, and want to learn how to use it to visualize simulation output from Gromacs. As a general tip, on the course machines you want to make sure that the rendering mode is set to GLSL to get the full benefit from the graphics boards. Feel free to ask questions also on topics not directly covered by the exercises. It is possible to continue working on the basic exercises also in the afternoon session. Choose the parts that you feel would be most useful to you. There is a lot of material, and if you are new to VMD, it is not likely that you manage to do everything in the allocated time. For other exercises, it is possible to do them using your own simulation results, or using a provided trajectory of a large membrane protein. For the official VMD tutorials, all input data is provided. Basic knowledge of Gromacs is assumed, but feel free to ask during the tutorial if you have not used Gromacs earlier.

Part of the exercises is formed by official VMD tutorials, while other parts are specifically written to put emphasis on how to use certain features of VMD and how to use VMD to visualize results produced by Gromacs. No previous knowledge of VMD is assumed, but there should be challenging exercises also for those who already know the basics of using VMD. General Information The goal of this tutorial is to give an overview of the features available in VMD. VMD Tutorial CSC, Espoo, Finland October 29, 2010

Vmd tutorial