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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 03 2023 - 02:00:02 PST
