Re: [gmx-users] connectivity issue
Hello, Just double check during the production phase too.You are welcome ! Παρακαλώ > On 14 Dec 2018, at 12:45, antonia vyrkou wrote: > > Hello Eleni, > > Thank you for your reply. I actually thought about that possibility after I > posted my problem and since I've triple checked my input files I assume > that's what is going on. > Thanks again! > Ευχαριστώ! > > Best regards, Antonia > > On Fri, Dec 14, 2018 at 12:39 PM Fitsiou, Eleni > wrote: > >> I think it is probably a visualisation issue ..If the bond is not in the >> topology, then you are fine. VMD for example uses a criterion based on the >> distance to show the bonds. >> >> Best, Eleni >>> On 14 Dec 2018, at 11:12, antonia vyrkou wrote: >>> >>> Hello, >>> >>> I am a bit puzzled by the following problem >>> >>> After the energy minimization, in one type of molecules, appear two >> bonds >>> that should not exist. If I visualize the pdb before the minimization >>> everything is normal. After the minimization this problem appears. >>> I checked the ffbonded.itp, the aminoacids.rtp, and the the .itp files, >> and >>> all connectivity is normal. >>> >>> Any ideas? >>> -- >>> 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.
Re: [gmx-users] connectivity issue
Hello Eleni, Thank you for your reply. I actually thought about that possibility after I posted my problem and since I've triple checked my input files I assume that's what is going on. Thanks again! Ευχαριστώ! Best regards, Antonia On Fri, Dec 14, 2018 at 12:39 PM Fitsiou, Eleni wrote: > I think it is probably a visualisation issue ..If the bond is not in the > topology, then you are fine. VMD for example uses a criterion based on the > distance to show the bonds. > > Best, Eleni > > On 14 Dec 2018, at 11:12, antonia vyrkou wrote: > > > > Hello, > > > > I am a bit puzzled by the following problem > > > > After the energy minimization, in one type of molecules, appear two > bonds > > that should not exist. If I visualize the pdb before the minimization > > everything is normal. After the minimization this problem appears. > > I checked the ffbonded.itp, the aminoacids.rtp, and the the .itp files, > and > > all connectivity is normal. > > > > Any ideas? > > -- > > 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.
Re: [gmx-users] connectivity issue
I think it is probably a visualisation issue ..If the bond is not in the topology, then you are fine. VMD for example uses a criterion based on the distance to show the bonds. Best, Eleni > On 14 Dec 2018, at 11:12, antonia vyrkou wrote: > > Hello, > > I am a bit puzzled by the following problem > > After the energy minimization, in one type of molecules, appear two bonds > that should not exist. If I visualize the pdb before the minimization > everything is normal. After the minimization this problem appears. > I checked the ffbonded.itp, the aminoacids.rtp, and the the .itp files, and > all connectivity is normal. > > Any ideas? > -- > 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.
