[AMBER] A question about PCA analysis

From: Markowska <markowska.kar.gmail.com>
Date: Tue, 18 Oct 2016 12:06:27 +0200

Dear Amber Users

I went through the PCA analysis tutorial:
http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/ and I have some

1. What can I learn from the histograms? What is on the x and y axis?
2. Is 'createcrd' command necessary? If I am using just one trajectory file
do I need to 'createcrd' and everytime use 'crdaction'? For my short, test
simulation I got a message from cptraj:
    1ryi-trajectories "1ryi-trajectories" (coordinates), size is 10000
(5361.33 MB) Box Coords, 46846 atoms
3. Are the frames obtained after projection real frames from my simulation?
4. A friend of mine found this paper:
http://onlinelibrary.wiley.com/doi/10.1002/chem.201602923/abstract and I'm
curious, how could I calculate the vibrational modes in my simulations?
Which command should I use for that?

Thank you very much for your help.
Have a nice day!
Karolina MitusiƄska
PhD student
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Received on Tue Oct 18 2016 - 03:30:03 PDT
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