Hi, Off-list Ali sent me a link to his movie - this does indeed show the ligand diffusing out gradually, rather than "jumping" in a discrete step. Such an event would be very rare for a lot of bound ligands with a suitable model physics, so if it's reproducible then you have problems with the model, somehow.
Mark On Fri, Apr 15, 2016 at 3:30 PM Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Please see > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > Mark > > On Fri, Apr 15, 2016 at 12:22 PM ali osouli <aliosouli...@gmail.com> > wrote: > >> Dear all >> My MD run movie shows that my ligand jump out of protein in the early >> picoseconds of simulation, does anybody knwos which step of my MD should i >> check? >> In additon to rutin steps i have included a distance restraint file to >> topolgy.itp. >> Best regards Ali >> -- >> 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.
