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. Austin- 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 <[email protected]> wrote: From: James Starlight <[email protected]> Subject: [gmx-users] analysis of the PCA projections To: "Discussion list for GROMACS users" <[email protected]> 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, James -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
