[gmx-users] Regarding PCA and Gibbs Free energy landscape

[bipin singh]

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 using gromacs.Now
on this landscape I want to map the conformation(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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Regards,
Bipin Singh