[gmx-users] analysis of the PCA projections

Austin B. Yongye ybausty at yahoo.com
Wed Feb 20 21:13:51 CET 2013

Hi James,After doing your 2D projections with g_anaeig, determine the x-y boundaries of your "transition state" from the plots.Your next task will be to generate indices corresponding to the frames you want to extract. You can store these indices in a file named frames.ndx (for example). The file format is:[ frames ]  1  6  etc for the frames
Proceed as follows:- write a script that scans the x-y values in the output file you specified using the -2d option when you ran g_anaeig. - when an x-y pair satisfies the boundaries of your "transition state," save its index in the frames.ndx file. Note that the index (from 1 to the total number of frames) is just a counter that is incremented every time you evaluate a new pair of x-y values.
Finally, run trjconv with your MD trajectory file and include the -fr frames.ndx option. The output file will contain your desired frames.
PS. These authors describe what you are trying to do, amongst other things:Deconstructing the native state: energy landscapes, functions, and dynamics of globular proteins. Zhuravlev, PI; Materese, CK; Papoian, GA. J. Phys. Chem. B 2009, 113, 8800-8812

--- On Mon, 2/18/13, James Starlight <jmsstarlight at gmail.com> wrote:
From: James Starlight <jmsstarlight at gmail.com>
Subject: [gmx-users] analysis of the PCA projections
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, February 18, 2013, 11:51 PM

Dear Gromacs users!

Commonly I analyze my MD trajectories by means of covariance analysis
(projections onto some PC made by g_anaiegn).

>From that projections I've often observe several highly populated
basins corresponded to the most populated regions of the collective
space where the system spend most time. Besides  there are some narrow
regions beetwen that basins which must correspond to the transition
(unstable) state. Now I'd like to "catch"  conformers from my md
trajectory corresponded to that "transition state" (simple to extract
it from my trajectory in the pdb files). How I could define the exact
time step or frame number of the specified regions on the PCA
projections ?

Thanks for help,

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