[AMBER] PCA eigenvalues

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Sat, 18 Nov 2017 15:05:51 +0000

Hi Amber users,

I have performed PCA analysis on my MD trajectories in cpptraj and would like to plot the fraction of total variance vs eigenvalue as shown in figure s9 of Roe et al 2014 (j phys chem b, 118, 3543-3552).
I also want to have a scatter plot of pc1 vs pc2 and pc2 vs pc3 to visualize clusters in this space.
Could someone please guide me in how this can be accomplished?
Also, how should the pca histogram analysis be interpreted?

This is my pca script:

trajin traj.nc

rms first :1-720&!.H=

average crdset Ndom_average

createcrd Ndom_trajectories


crdaction Ndom_trajectories rms ref Ndom_average :1-720&!.H=

crdaction Ndom_trajectories matrix covar name Ndom_covar :1-720&!.H=

runanalysis diagmatrix Ndom_covar out Ndom_evecs.dat vecs 20 name NdomEvecs nmwiz nmwizvecs 3 nmwizfile Ndom_pca.nmd nmwizmask :1-720&!.H=

crdaction Ndom_trajectories projection Ndom modes NdomEvecs beg 1 end 3 :1-720&!.H= crdframes 1,3000

hist Ndom:1 bins 100 out Ndom_hist.agr norm name Ndom_1

hist Ndom:2 bins 100 out Ndom_hist.agr norm name Ndom_2

hist Ndom:3 bins 100 out Ndom_hist.agr norm name Ndom_3


clear all

readdata Ndom_evecs.dat name Evecs

parm NDOM_CPLX_rnb_stripped_box.prmtop

parmstrip !(:1-720&!.H=)

parmwrite out Ndom_modes.prmtop

runanalysis modes name Evecs trajout Ndom_mode1.nc pcmin -100 pcmax 100 tmode 1 trajoutmask :1-720&!.H= trajoutfmt netcdf

runanalysis modes name Evecs trajout Ndom_mode2.nc pcmin -100 pcmax 100 tmode 2 trajoutmask :1-720&!.H= trajoutfmt netcdf

runanalysis modes name Evecs trajout Ndom_mode3.nc pcmin -100 pcmax 100 tmode 3 trajoutmask :1-720&!.H= trajoutfmt netcdf

Kind regards

Lizelle Lubbe
PhD Chemical Biology candidate
University of Cape Town
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Received on Sat Nov 18 2017 - 07:30:03 PST
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