# AMBER: correlation along PCA modes

Date: Mon, 07 Feb 2005 12:35:44 +0100

Dear Amber users,
I am trying to calculate the correlation between 2 defined vecors
along different modes from PCA. I am interested in the difference
between the correlation of the 2 vecs along the first mode and the same
correlation along the second mode. Surprizingly, the 2 correlations are
identical (when comparing "ga1-kt-corr-1.dat" with "ga1-kt-corr-2.dat"
-- see below). From the structure visualization it is clear that this is
not the case. So, I am wondering what do I do wrong here? The ptraj
input file is below. I would appreciate any suggestions on this.
Thanks
A nice week to everybody

trajin traj.mdcrd

vector v11 :7.N2 corr :19.N7 order 2 modes evecs.pev beg 1 end 1
vector v21 :18.N2 corr :8.N7 order 2 modes evecs.pev beg 1 end 1
vector v31 :10.P corr :22.P order 2 modes evecs.pev beg 1 end 1

analyze timecorr vec1 v11 vec2 v31 out ga1-kt-corr-1.dat
analyze timecorr vec1 v21 vec2 v31 out ga2-kt-corr-1.dat

vector v12 :7.N2 corr :19.N7 order 2 modes evecs.pev beg 2 end 2
vector v22 :18.N2 corr :8.N7 order 2 modes evecs.pev beg 2 end 2
vector v32 :10.P corr :22.P order 2 modes evecs.pev beg 2 end 2

analyze timecorr vec1 v12 vec2 v32 out ga1-kt-corr-2.dat
analyze timecorr vec1 v22 vec2 v32 out ga2-kt-corr-2.dat

vector v13 :7.N2 corr :19.N7 order 2 modes evecs.pev beg 3 end 3
vector v23 :18.N2 corr :8.N7 order 2 modes evecs.pev beg 3 end 3
vector v33 :10.P corr :22.P order 2 modes evecs.pev beg 3 end 3

analyze timecorr vec1 v13 vec2 v33 out ga1-kt-corr-3.dat
analyze timecorr vec1 v23 vec2 v33 out ga2-kt-corr-3.dat

go

```--