Hello, I have done PCA using cartesian coordinates by the help of gromacs(g_covar and g_anaeig), then using the 2-d projection of trajectory on first two eigenvectors as reaction coordinates,I have calculated a 2-d representation of the gibbs free energy landscape(g_sham) using gromacs.Now on this landscape I want to map the conformations(structures from the MD trajectories) of the protein onto the different region(for eg:minima)of this landscape. Please suggest how can I perform this task....
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