Hi, It sounds like you are observing artefacts from http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan <zruan1...@gmail.com> wrote: > Hi Gromacs Users, > > I'm running 20ns MD simulation of a protein kinase with ATP bond. I use > amber99sb-ildn force field with parameters of ATP derived from the database > of Richard Bryce. > > What surprised me is that the ATP molecules displays a huge flexibility and > conformational change. First, it slipped out from the starting binding > pocket. In addition, the plane of adenine ring and ribose sugar rotate to > about 180 degree after 10ns, making the ATP molecule looks weird. I never > run a MD of a protein with ligand before. Is this something normal? What > are possible causes for this? Maybe I should try some other ATP protein > complex to see if the same thing happens? Thank you! > > Ruan > -- > 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.