On 5/2/20 3:12 PM, lazaro monteserin wrote:
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 dangle.ndx from my MD
in the file (*dangle.trr*) with the following command:
*gmx angle -f md_5ns.xtc -n dangle.ndx -or dangle.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 dangle.trr -s md_5ns.tpr -o resized.gro -n covar.ndx -e
10000 was the time in ps for the last frame of the simulation.

5) I runned covar:
*gmx covar -f dangle.trr -s resized.gro -n covar.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 eigenvec.trr -f dangle.trr -s resized.gro -first 1 -last 2
-2d 2dproj_1_2.xvg*

7) Then I got the projection in 3D of the free energy landscape:
*gmx sham -f 2dproj_1_2.xvg -notime -bin bindex-1_2.ndx -lp prob-1_2.xpm
-ls gibbs-1_2.xpm -lsh enthalpy-1_2.xpm -g shamlog-1_2 -lss entropy-1_2.xpm*

Note: I attached all the files in the dropbox link below

I can't access the Dropbox folder because you have given permission for the mailing list email to access it. Please either make it public or upload to a different service. The most relevant files are 2dproj_1_2.xvg and gibbs-1_2.xpm



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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