This is very helpful thank you. I think I can use this. I will also ask the vmd mail list.
Best, Miro Le mer. 15 janv. 2020 à 19:35, Alessandra Villa < alessandra.villa.bio...@gmail.com> a écrit : > Hi, > One of the criteria that VMD uses to define bond is distance criteria. When > you source your gro file, this criteria is applied. > One way one, I have used is to not visualize undesired bonds, is the > following: > delete the undesired bonds, save the vmd setting (*.vmd file), load the > setting before any of the following visualizations. > That is not the most elegant way, but it works in my case. > For more elegant ways, you could ask to VMD maillist. > Best regards > Alessandra > > > On Tue, Jan 14, 2020 at 8:59 PM Miro Astore <miro.ast...@gmail.com> wrote: > > > Hi kenny, thanks for getting back to me. > > > > I use something similar to what you've suggested to deal with periodic > > boundary conditions. My current issue is that vmd will place a bond > between > > two atoms that are close together in the first frame of the visualization > > even if those atoms aren't linked in the topology. The fake bonds are > then > > kept throughout the visualization . That is, when I load just a gro and a > > trr. > > > > A psf file would fix this situation but my efforts to recreate a whole > one > > from my complex system using top2psf.pl hasn't borne much fruit. > > > > Just wondering what other people have tried. > > > > Best, Miro > > > > Le mer. 15 janv. 2020 à 02:20, Kenny Goossens < > goossens_ke...@hotmail.com> > > a écrit : > > > > > Hi, > > > > > > I'm not sure what you mean by "bonds that aren't in the simulation", > but > > > from my experience, converting your .gro file with gmx trjconv using > the > > > -pbc mol and -ur compact options usually gives a clean visualisation. > If > > > necessary, you can also use the -center option to center a specific > > > structure/residue in the box. You can have the output written in the > .gro > > > file format, or convert to anything more convenient. > > > > > > With kind regards, > > > ______________________________ > > > Kenneth Goossens, PhD student > > > Laboratory of Medicinal Chemistry (Building A - Room 2.13) > > > University of Antwerp - Campus Drie Eiken > > > Universiteitsplein 1 > > > B-2610 Wilrijk > > > Belgium > > > > > > > > > > > > ________________________________ > > > Van: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> namens Miro Astore > < > > > miro.ast...@gmail.com> > > > Verzonden: dinsdag 14 januari 2020 3:48 > > > Aan: gromacs.org_gmx-users@maillist.sys.kth.se < > > > gromacs.org_gmx-users@maillist.sys.kth.se> > > > Onderwerp: [gmx-users] Loading topology into vmd > > > > > > Hello all, > > > > > > I'm just wondering how people load topologies for systems simulated in > > > gromacs into vmd. It is very annoying to have bonds that aren't in the > > > simulation placed in the visualisation. I'm wondering if anyone has a > > > solution that is easier than simply creating a psf file of the .gro > > system > > > as this can be time consuming for systems with strange geometries. > > > > > > Best, Miro > > > -- > > > 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. > > > > > -- > > 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. -- 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.
