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? 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. > -- 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.
