I was recently told in passing that it would be possible to construct a 'potential energy landscape' from the simulations I have performed. This way I could remove any loading rate differences between simulations and experimental force experiments I've been performing ... however I cannot find anywhere in which this is mentioned.
The only thing close I could find that was close was the free energy landscape using g_anaeig under the Dihedral PCA (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure this is what I'm looking for. Does anyone know where I would be able to find out / read more about how to create potential energy landscapes from my simulation outputs? Thanks Natalie
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