[gmx-users] analysis of the PCA projections

James Starlight jmsstarlight at gmail.com
Tue Feb 19 08:51:00 CET 2013

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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