AMBER Archive (2005)

Subject: AMBER: correlation along PCA modes

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Mon Feb 07 2005 - 05:35:44 CST

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
vlad

trajin traj.mdcrd

vector v11 :7_at_N2 corr :19_at_N7 order 2 modes evecs.pev beg 1 end 1
vector v21 :18_at_N2 corr :8_at_N7 order 2 modes evecs.pev beg 1 end 1
vector v31 :10_at_P corr :22_at_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_at_N2 corr :19_at_N7 order 2 modes evecs.pev beg 2 end 2
vector v22 :18_at_N2 corr :8_at_N7 order 2 modes evecs.pev beg 2 end 2
vector v32 :10_at_P corr :22_at_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_at_N2 corr :19_at_N7 order 2 modes evecs.pev beg 3 end 3
vector v23 :18_at_N2 corr :8_at_N7 order 2 modes evecs.pev beg 3 end 3
vector v33 :10_at_P corr :22_at_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 

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
home tel: ++49-551-9963204  

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