Re: [AMBER] A question about PCA analysis

From: Hai Nguyen <>
Date: Mon, 24 Oct 2016 17:48:59 -0400


On Tue, Oct 18, 2016 at 6:06 AM, Karolina Mitusińska (Markowska) <> wrote:

> Dear Amber Users
> I went through the PCA analysis tutorial:
> and I have some
> questions.
> 1. What can I learn from the histograms? What is on the x and y axis?

It would be best to read two listed papers in that tutorial.

> 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

"createcrd" will load all trajectory into memory. So it's much faster to
iterate frames (with the cost of memory).
You can check amber manual for further info.

By the way, for all of your questions, Dan Roe is probably the best person
to reply.

> 3. Are the frames obtained after projection real frames from my simulation?
> 4. A friend of mine found this paper:
> 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 Mitusińska
> PhD student
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Received on Mon Oct 24 2016 - 15:00:02 PDT
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