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

[Dallas Warren]

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.baydan at 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
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