[gmx-users] Lazaro Andres Monteserin Castanedo shared "dPCA" with you

[Lazaro Andres Monteserin Castanedo (via Dropbox)]

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&#58;&#10;&#10;I followed the protocol in gromacs website to do dihedral Principal Component Analysis&#58;&#10;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.&#10;&#10;2) Then I extracted the sin&#47;cos of the angles in the <span>dangle</span>.ndx from my MD in the file (dangle.trr) with the following command&#58;gmx angle -f md_<span>5ns</span>.xtc -n <span>dangle</span>.ndx -or <span>dangle</span>.trr -type dihedral&#10;&#10;(I had 21 angles so it used 14 sin&#47;cos to represent the angles)&#10;3) Then I generated an index file (covar.ndx) with a list of numbers from 1 to 14 for trjconv.&#10;&#10;4) I runned trjconv to generate the dummy (resized.gro) to use for the covariance analysis&#58;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.&#10;&#10;5) I runned covar&#58;gmx covar -f <span>dangle</span>.trr -s <span>resized</span>.gro -n <span>covar</span>.ndx -ascii -xpm -nofit -nomwa -noref -nopbc&#10;&#10;6) Then I got the PMF along one eigenvector and 2D free energy landscape for projections along two eigenvectors&#58;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&#10;&#10;7) Then I got the projection in 3D of the free energy landscape&#58;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&#10;&#10;&#10;I would appreciate any feedback&#10;Thank you in advance Dr. Lemkul&#10;Kindly,&#160;Lazaro"

Go to folder[1]

Enjoy!
The Dropbox team

[1]: https://www.dropbox.com/l/scl/AACmJPduzqbNRmC7scaafSZ0pkU9B-KtLvo