[AMBER] PCA porjection & representative structure

From: Hocine EL KHAOUDI ENYOURY via AMBER <amber.ambermd.org>
Date: Fri, 3 Feb 2023 10:40:50 +0100

Dear amber community,

Im trying to perform a PCA, and plot the projection using the following script:

parm complex.psf
trajin complex.dcd
trajin complex.dcd
trajincomplex.dcd

rms first .CA
average crdset avg_set

createcrd traj_set

run

crdaction traj_set rms ref avg_set .CA

crdaction traj_set matrix covar :.CA name pro_covar out covmat.dat

runanalysis diagmatrix pro_covar out evecs.dat vecs 100 name myevecs nmwiz nmwizvecs 100 nmwizfile complex.nmd nmwizmask :.CA
runanalysis modes eigenval name myevecs out evalfrac.dat
runanalysis modes fluct out rmsfluct1-10.dat name
myevecs beg 1 end 10 #to write the fluctuations of first 10 PCs

runanalysis modes fluct out rmsfluct1-2.dat name myevecs beg 1 end 2

runanalysis modes fluct out rmsfluct-mode1.dat name myevecs beg 1 #to write the fluctuations of first PC

crdaction traj_set projection p1 modes myevecs beg 1 end 20 .CA out pca.dat #to write the projections
of first 20 PCs

crdaction traj_set projection p2 modes myevecs beg 1 end 2 :.CA out pca12.dat #to write the projections of first 2
PCs

runanalysis hist p1:1 p1:2 bins 100 free 300 out fhist-all.CA.agr

Is there a way to extract a representative structure of each bin of the plot?


Thanks!

Hocine
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Received on Fri Feb 03 2023 - 02:00:02 PST
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