[gmx-users] PCA analysis and comparing extreme1 pdbs of two different simulations

[Prasanth G, Research Scholar]

Dear all,

I am interested in carrying out PCA analysis on two trajectories- 1)
protein in water and 2) protein with ligand in water.
I would like to know, if there is a procedure by which we can compare the
extreme1 pdbs (constituted by the movements that contribute to EV1) from
both the trajectories.
If yes, do we need to concatenate both the trajectories? I would be
grateful if you could share some of your ideas on this matter.

Thank you. Regards.


-- 
Regards,
Prasanth.