(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015

TUTORIAL B2 - SECTION 9

Using VMD with AMBER

By Ross Walker

9) Creating a Movie

Finally lets learn how to create a movie of our trajectory so that we can use it in a talk. Note, this may not work on all systems due to compatibility of various compression codecs. However, give it a try on your system and see how you get on. Start by Clicking Extensions->Visualization->Movie Maker.

There are a large number of different options available here. I won't try and cover all the options, see the VMD website for more information. In this example I shall just just step through creating a simple movie of the trajectory. Start by picking a suitable working trajectory. The screen shots here are from the Unix version of VMD. It may look slightly different in Mac and Windows.

Next enter a name for the movie, e.g. TRPcage. We next need to pick the duration of the movie, based on the number of frames we want. The movie will be playing at 24 frames per second. (See Format->Change Compression Settings for the frame rate). Hence 400 frames will give us about 16 seconds for our movie, which is reasonable. If we wanted it to last around 8 seconds, we could cut the number of frames to 200 and we would get every other frame rendered. Alternatively we could set it to 32 seconds and get an 800 frame movie. The movie length is something you should always consider since it needs to be compatible with your talk. So, enter 16 in the "Movie duration (seconds):" box. We want every frame of the trajectory so leave the step size at 1.

Next we want just a single run through of our trajectory so select Movie Settings->Trajectory. Then under Format select MPEG-1. This will create an MPEG-1 format video file. By all means play about with the AVI format if you want.

Then hit on "Make Movie". Hopefully after about 3 minutes or so you should find a movie file in your working directory.

Here it is TRPcage.mpg (2.9 mb)

This ends the tutorial. This hopefully has given you the knowledge you need view and analyze AMBER files and trajectories using VMD. Bear in mind, however, that we have not even scratched the surface in terms of what VMD can do. If you go to the VMD website you will find much more information covering the more advanced features in VMD.

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(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015