[gmx-users] issues by simulating adsorption of peptide on a polymer surface

[Baydan, Sezai-Raif]

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