Hi Nikhil, Lazaro Andres Monteserin Castanedo (lamonteserincastan...@gmail.com) invited you to edit the folder " dPCA " on Dropbox.
Lazaro Andres said: "Dear Dr. Lemkul I used the following protocol to generate the (.xpm) files: I followed the protocol in gromacs website to do dihedral Principal Component Analysis: 1) Created an index file (dangle.ndx) with a list of the dihedrals to analyze from my molecule. I wrote this file in a text editor by hand as we discussed before. 2) Then I extracted the sin/cos of the angles in the <span>dangle</span>.ndx from my MD in the file (dangle.trr) with the following command:gmx angle -f md_<span>5ns</span>.xtc -n <span>dangle</span>.ndx -or <span>dangle</span>.trr -type dihedral (I had 21 angles so it used 14 sin/cos to represent the angles) 3) Then I generated an index file (covar.ndx) with a list of numbers from 1 to 14 for trjconv. 4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis:gmx trjconv -f <span>dangle</span>.trr -s md_<span>5ns</span>.tpr -o <span>resized</span>.gro -n <span>covar</span>.ndx -e 1000010000 was the time in ps for the last frame of the simulation. 5) I runned covar:gmx covar -f <span>dangle</span>.trr -s <span>resized</span>.gro -n <span>covar</span>.ndx -ascii -xpm -nofit -nomwa -noref -nopbc 6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors:gmx anaeig -v <span>eigenvec</span>.trr -f <span>dangle</span>.trr -s <span>resized</span>.gro -first 1 -last 2 -2d 2dproj_1_<span>2</span>.xvg 7) Then I got the projection in 3D of the free energy landscape:gmx sham -f 2dproj_1_<span>2</span>.xvg -notime -bin bindex-1_<span>2</span>.ndx -lp prob-1_<span>2</span>.xpm -ls gibbs-1_<span>2</span>.xpm -lsh enthalpy-1_<span>2</span>.xpm -g shamlog-1_2 -lss entropy-1_<span>2</span>.xpm I would appreciate any feedback Thank you in advance Dr. Lemkul Kindly, Lazaro" Go to folder[1] Enjoy! The Dropbox team [1]: https://www.dropbox.com/l/scl/AACmJPduzqbNRmC7scaafSZ0pkU9B-KtLvo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
