Hi, This is entirely normal. Please see http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark On Thu, Apr 20, 2017 at 9:16 AM abhisek Mondal <abhisek.m...@gmail.com> wrote: > Hi, > > I'm trying to simulate a protein for 40ns after 20ns nvt and 20ns npt > equilibration, respectively. After nvt and npt equilibration steps the > protein looks fine to me. But when I analyze the trajectory file generated > after 40ns of production run, I found some unusual facts. > Half of the trajectory seems fine, then suddenly the loops and sheets of > the protein got elongated and after some time it came back to normal. > > Can you please tell me is there any mistake I'm making during simulation ? > I have kept a screenshot of elongated-protein (trajectory snapshot) in the > following link: > https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0 > > The backbone RMSD (after production run) seems to fluctuate at the > beginning but reached some stable value after sometime and so does the > radius of gyration. > > Please suggest me a way out. > > Thanks > > -- > Abhisek Mondal > > *Senior Research Fellow* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *INDIA* > -- > 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.