[gmx-users] clarity w.r.t pca analysis of protein and ligand complex

[Prasanth G, Research Scholar]

Dear all,

I am interested in carrying out PCA analysis of protein and ligand complex
in order to understand which ligand binds to protein and restricts the
relative movement of the chains of receptor during simulation.
I have carried out four simulations of 30 ns each -
1) with just the protein (receptor) in water
2) ligand A with receptor
3) ligand B with receptor and
4) ligand C with receptor.

If i am interested in comparing the effectiveness of ligand binding. Should
I, use the NPT.pdb obtained from the 1st simulation as a reference to check
the covariance of the backbone
or
Should it be the NPT.pdb obtained in the individual simulations?

-- 
Regards,
Prasanth.