Hi,
I'm not sure where you got that syntax, but that's not something
cpptraj will understand.
I never got around to doing a straight dot product for eigenvectors,
but to compare two sets of eigenvectors you can calculate the
root-mean-square inner product (rmsip) which of course is made up of
dot products:
# Read in previously generated eigenvectors
readdata evecs.dat name MyModes1
readdata evecs.dat name MyModes2
# Calculate the RMSIP for only the first mode
runanalysis modes rmsip setname FirstMode name MyModes1 name2 MyModes2
beg 1 end 1 out rmsip.dat
runanalysis modes rmsip setname FiveModes name MyModes1 name2 MyModes2
beg 1 end 5 out rmsip.dat
Hope this helps!
-Dan
PS - for more info on generating eigenvectors (i.e. running PCA) see
here: https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/
On Wed, Dec 10, 2025 at 10:30 PM Osman, Roman via AMBER
<amber.ambermd.org> wrote:
>
> Hello,
>
> I would like to calculate the dot product between eigenvectors from two separate PCA on the same protein.
> I found these instructions:
>
> * Load both sets of modes: load traj1.nc, load traj2.nc.
> * Use vectormath to calculate the dot product or angle. For example, to compare the first mode of each set:
>
> vector v1 = modes1[1] // First mode from modes1.nc
> vector v2 = modes2[1] // First mode from modes2.nc
> vectormath vec1 v1 vec2 v2 dotproduct [out dot1.dat]
>
>
> It all makes sense in principle, except for the definitions of the vectors (the = sign). How do I equate vector v1 with the first eigenvector?
>
>
> Roman Osman
>
> Professor
>
> Department of Pharmacological Sciences
>
> Icahn School of Medicine at Mount Sinai
>
>
>
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Received on Thu Dec 11 2025 - 06:00:02 PST
