[gmx-users] Principal component analysis

Upendra N 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

With Regards
Upendra N
Research Scholar
Department of Studies in Physics,Manasagangotri
University of Mysore, Mysuru

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