Have you checked to see if it is in fact actually moving away, and not a periodic boundary condition visualisation issue?>
This may help with understanding what is going on …. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-September/115927.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Thu, 11 Oct 2018 at 20:05, Antonio Carlesso <antonio.gromacs.carle...@gmail.com> wrote: > > Hi all, > > we have some problem in correctly reimaging a protein-multiple ligands MD > simulations. > > Since we were trying in investigating the recognition process some ligands > “fly away” from the binding region and going out from the box (10 Å length). > > When calculating the distance over time between two pair of atoms using gmx > distance the analysis does not match with the value obtained in VMD and > with snaphots downloaded every 100 ns.. > > > > > > Do you have any idea how to fix this issue? > > Thank you! > -- > 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.