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2024-05-07
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2024-05-06
Editing Anisotropic fluctuations (and their visualisation)
/trio/, /gromacs/ and /Raster3D/ : * Start from *my.dcd* and a PDB file (say, *my.pdb*) containing a set of atoms corresponding to those present in the DCD file (for example, from psfgen). * Convert the DCD file to a format understood by /gromacs/ : <code> trio my.dcd my.g96 </code> * Run <b>g_rmsf</b> (from the /gromacs/ suite) : <code> /usr/local/gromacs/i686-pc-linux-gnu/bin/g_rmsf -f my.g96 -s my.pdb -oq aniso.pdb -aniso </code> * If all goes well, try to make a picture of it : <code> rastep -nohydrogens -fancy3 < aniso.pdb | render -size 1024x1024 -zoom 1.5 -jpeg picture.jpg ; display picture.jpg </code> [[image: molecular dynamics anisotropic thermal ellipsoids 2]] [[image: molecular dynamics anisotropic thermal ellipsoids 1]]
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