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From: Vlad Cojocaru <Vlad.Cojocaru.mpi-bpc.mpg.de>

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

vlad

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

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

vlad

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

-- 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.mpi-bpc.mpg.de home tel: ++49-551-9963204 ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Mon Feb 07 2005 - 11:53:01 PST

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