AMBER Archive (2005)Subject: AMBER: correlation along PCA modes
From: Vlad Cojocaru (Vlad.Cojocaru_at_mpibpc.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 "ga1ktcorr1.dat" with "ga1ktcorr2.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 ga1ktcorr1.dat
analyze timecorr vec1 v21 vec2 v31 out ga2ktcorr1.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 ga1ktcorr2.dat
analyze timecorr vec1 v22 vec2 v32 out ga2ktcorr2.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 ga1ktcorr3.dat
analyze timecorr vec1 v23 vec2 v33 out ga2ktcorr3.dat
go

Vlad Cojocaru
Max Planck Institute for Biophysical Chemistry
Department: 060
Am Fassberg 11, 37077 Goettingen, Germany
tel: ++49551201.1327
email: Vlad.Cojocaru_at_mpibpc.mpg.de
home tel: ++495519963204

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