[gmx-users] Lazaro Andres Monteserin Castanedo shared "dPCA" with you
Lazaro Andres Monteserin Castanedo (via Dropbox)
no-reply at dropbox.com
Sat May 2 21:12:03 CEST 2020
Hi Nikhil,
Lazaro Andres Monteserin Castanedo (lamonteserincastanedo at 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
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