[gmx-users] Visualisation of free energy diagrams by gmx sham

James Starlight jmsstarlight at gmail.com
Thu Mar 28 14:37:57 CET 2019

Dear Gromacs users!

I am performing PCA via gmx covar -and  gmx anaeig and then obtain 2D
free energy plot by gmx sham.
How it would be possible to establish which conformation in the
ensemble of the filtered trajectory (produced by gmx anaeig-filt
ensemble.pdb) corresponds to the each point on the 2D projection (e.g.
to indicate its as a layer)?
Wouls it be possible also to project some x-ray structure onto the
same ensemble/ 2D plot to use it as a reference point with the
indication of the layer?

Thanks in advance!

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