[gmx-users] question about how to analyze the free energy landscape generated with gmx sham

lazaro monteserin lamonteserincastanedo at gmail.com
Sun May 3 23:40:52 CEST 2020

Dear Gromacs users;

I have generated Gibbs free energy landscapes from the two first principal
components PC1 and PC2 obtained from Dihedral Principal Component analysis
performed using Gromacs.

So, now I have a file *"shamlog-1_2.log" *that contain a list of the bins
ordered by energy, for example :
Minima sorted after energy
Minimum 0 at index 40 energy      0.000
Minimum 1 at index 641 energy      0.146 (...)
and I have another file *bindex-1_2.ndx* that shows the frames contained in
each bin.
Now I do not know how to proceed from here. How do I select the best bins?
and then how do I select the best frames from those bins? Should I use all
the frames of the selected bins and obtain like an average structure?
Kindly, Lazaro

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