You are going to have to show what these "artefacts" are, as from what you have written it is not clear what you are referring to.
On Mon, 4 Nov. 2019, 6:15 am Baydan, Sezai-Raif, < sezai-raif.bay...@rwth-aachen.de> wrote: > Hello! > > > I have some issues with my simulation. I am trying to simulate the > interaction of an peptide on a polymer surface. For that I restrain both, > the peptide and the polymer for the equilibration steps, otherwise the > polymer-layer destabilizes. For the final run, I only restrain the polymer. > > > After I run my simulation for 100 ns, I can see some artifacts shifting > over my peptide! But it is not really artifacts because they are coming > back to their origin places. It is just for few nanoseconds but it is > repeating again and again. So my peptide can not adsorb on the surface, > because some 'artifacts' (shifting up and down) are pulling my peptide > away from the surface. > > > First I thought it is a visualization problem and I tried to fix it by > using different pbc options. But actually, the peptide is interacting with > these 'ghost-artifacts'. > > I realized, that the md.gro file (without including any .xtc file) shows > me a monatomic layer over me peptide! But my set-up is such that my layer > is below my peptide and even below the layer there is nothing, not even > water molecules. The box I have generated so that it is sufficiently large, > so that the layer fits exactly into the pbc box. > > > However, I do not know if this monatomic layer and the ghost artifacts are > related, or if these are actually two separate issues. How can I solve > these issues? > > > Yours sincerely, > > Sezai Baydan > -- > 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.