[gmx-users] about how to create angle.index with specific angles

Justin Lemkul jalemkul at vt.edu
Tue May 5 20:01:34 CEST 2020

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*
> 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
> https://www.dropbox.com/sh/wez43stnyv4ho31/AABQ3xwgUGf0CuMI_UF7MGsWa?dl=0

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

jalemkul at vt.edu | (540) 231-3129


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