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 would appreciate any feedback Thank you in advance Dr. Lemkul Kindly, Lazaro On Sat, May 2, 2020 at 8:47 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/30/20 2:07 PM, lazaro monteserin wrote: > > Dear Dr. Lemkul I did it. It works. Thank you very much for the advise. > > > > Now I am having issues opening the (.xpm) files generated that contain > for > > example the gibbs energy landscape on the two first eigenvectors of the > > dPCA. > > > > If I use the command "gmx xpm2ps -f gibbs-1_2.xpm -w yes -o > gibbs-1_2.eps" > > it write this error: "Input error or input inconsistency: > > Invalid XPixMap" > > > > Do you know if I am missing something here? Do I have to install > something > > in my OS to be able to see .xpm images? > > The error is coming from xpm2ps which means there's something wrong with > the .xpm file itself but without seeing how you generated it (exact > command and description of how you prepared the input data file) and > perhaps the .xpm file itself (uploaded somewhere), it's impossible to > comment further. > > -Justin > > > Thanks in advance, > > > > Lazaro > > > > On Wed, Apr 29, 2020 at 8:57 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 4/29/20 7:11 PM, lazaro monteserin wrote: > >>> Dear Dr. Lemkul it could be possible use that angle.index with the > >> selected > >>> dihedrals written by hand as index file for gmx angle for dihedral > >>> Principal Component Analysis? > >> You can create index groups however you like for whatever analysis you > >> want to perform. > >> > >> -Justin > >> > >>> Kindly, > >>> Lazaro > >>> > >>> On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul <jalem...@vt.edu> wrote: > >>> > >>>> On 4/29/20 5:01 PM, lazaro monteserin wrote: > >>>>> Dear gromacs users, > >>>>> > >>>>> Is there any way to tell gmx mk_angndx to create the index file with > >>>>> dihedral angles from a (.tpr) for specific atom numbers (atom level, > >> e.g > >>>> 1, > >>>>> 2, 3) from my molecule? > >>>> mk_angndx is designed for distributions of similar angles (e.g. > >>>> evaluating force field sampling). If you want to compute specific > >>>> angles, use make_ndx or simply write the index groups by hand. > >>>> > >>>> -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. > >>>> > >> -- > >> ================================================== > >> > >> 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. > >> > > -- > ================================================== > > 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. > -- 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.
