I think pulling code can solve the problem, http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling
On Fri, Mar 20, 2020 at 12:04 PM Oscar Hernandez Alba <ahernan...@unistra.fr> wrote: > Dear all, > > > > I am trying to run MD with a protein with four different chains. When > I > convert this structure to gromacs, I have four different molecules in the > topology file. I would like to use distance restraints between specific > atoms of different chains. I have created the itp file with the information > of the atoms involved in distance restraints. However, when I run the MD > simulation with distance restraints I always get the same error message : < > you have inserted topology section "distance_restraints" in a part > belonging > to a different molecule than you intended to >. Can someone help me with > this problem ? I do not what is the exact place of the < > distance-restraints > > section in the topology file. > > > > Thank you very much. > > > > Oscar > > -- > 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.
