[gmx-users] Projection of crystal structure on PCA plot

Anirban reach.anirban.ghosh at gmail.com
Thu Jun 6 12:06:25 CEST 2013


I have carried out a simulation of a protein and have carried out PCA on
the entire trajectory. I have obtained a 2D projection plot of EV1 on EV2.
Now I want to locate the conformation of the crystal structure (with which
I started the MD) on this map. How to do this? Can I use "g_anaeig -v
Prt_MD_Eigenvec.trr -s Prt.tpr -f crystal.pdb -proj 12.xvg -n Prt_CA.ndx
-first 1 -last 2 -2d 2dproj.xvg" to obtain the crystal structure position?
Or do I need to calculate covariance matrix for the crystal str.(I need a
set of them in that case) and then use g_anaeig?
Thanks a lot in advance.



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