[gmx-users] Principal component analysis
nupendra90 at gmail.com
Mon Jun 25 18:26:54 CEST 2018
Dear Gromacs Users,
I am trying to understand PCA. I have done 10ps(6 frames) simulation
for small peptide (4 residues ).
After obtaining trajectory, I Had carried out PCA for C-alpha atoms
using gmx covar and gmx anaeig.
In gmx anaeig i have selected first eigen vector for projection
and extracted extreme structures.
My doubt is, what mathematical operation does gromacs performs in order
to identify extreme values.
I tried matrix multiplication (using) of transpose of first eigen
vector to differnt frames arranged in column matrix.
In my case there are 12 elements for 4 c-alpha atoms.
Kindly clear my doubt.. what is the mathematical operation to be done to
determine extreme values.
Thanks in advance
Department of Studies in Physics,Manasagangotri
University of Mysore, Mysuru
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