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 -- ================================================== 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 http://www.thelemkullab.com ================================================== -- 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.