Hi ALL, 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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