The reason why we output DCD files is that MD simulations usually generate a large amount of coordinates trajectory data, and we want to keep the file size as small as possible. # Take a look at the contents in the DCD file $ less run.dcdĭCD files are binary data, and no human can see what is written in them. Let’s take a look at the DCD file using the less command. # Take a look at the trajectory using VMD The trajectory consists of 50 frames, generated from GENESIS and processed with the crd_convert tool, with the water and ions wrapped into unit cells. This is a very small system consisting of one protein (chignolin), water molecules, and ions, with a total of 2,382 atoms. In the directory, you will find the PDB and DCD files. ![]() Let’s download the tutorial file ( tutorial19-4.1.zip). In this tutorial, we will learn how to analyze coordinates data in DCD format by editing a simple sample Fortran program. If we want to analyze “minor” quantities that cannot be handled by the GENESIS analysis tools, we need to create your own tools or scripts. ![]() However, these are only for analyzing “major” quantities such as distance, angle, RMSD, etc. Various analysis tools are available in the GENESIS program package. After MD simulation, a DCD file is obtained as the coordinate trajectory data.
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