Hi,
To begin with PCA analysis, I followed following tutorial:
http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/
And I started as follows:
parm pt_nowat.prmtop
trajin pt-nowat.mdcrd 25000 50000 1
rms first :1-360&!.H=
average crdset pt-average
createcrd pt-trajectories
run
crdaction pt-trajectories rms ref pt-average :1-360&!.H=
crdaction pt-trajectories matrix covar name pt-covar :1-360&!.H=
runanalysis diagmatrix pt-covar out pt-evecs.dat vecs 3 name myEvecs nmwiz
nmwizvecs 3 nmwizfile pt.nmd nmwizmask :1-360&!.H=
crdaction pt-trajectories projection pt modes myEvecs beg 1 end 3
:1-360&!.H= crdframes 1,last
hist pt:1 bins 100 out pt-hist.agr norm name pt-1
hist pt:2 bins 100 out pt-hist.agr norm name pt-2
hist pt:3 bins 100 out pt-hist.agr norm name pt-3
run
clear all
readdata pt-evecs.dat name Evecs
parm pt_nowat.prmtop
parmstrip !(:1-360&!.H=)
parmwrite out pt-modes.prmtop
runanalysis modes name Evecs trajout pt-mode1.mdcrd pcmin -100 pcmax 100
tmode 1 trajoutmask :1-360&!.H= trajoutfmt mdcrd
runanalysis modes name Evecs trajout pt-mode2.mdcrd pcmin -100 pcmax 100
tmode 2 trajoutmask :1-360&!.H= trajoutfmt mdcrd
runanalysis modes name Evecs trajout pt-mode3.mdcrd pcmin -100 pcmax 100
tmode 3 trajoutmask :1-360&!.H= trajoutfmt mdcrd
exit
And I generated following files:
*pt-evecs.dat pt-hist.agr pt-mode1.mdcrd pt-mode2.mdcrd pt-mode3.mdcrd
pt-modes.prmtop*
I wonder, how can I see first 3 eigenvectors and calculate the %
contribution of each of them..
Thanks,
Hirdesh
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Received on Tue Jun 21 2016 - 06:00:03 PDT
