[gmx-users] polymer & peptide interaction pbc, visualization problem

[p buscemi]

I've run protein adsorptions on PE, PEO, nylon and the like. The way I approach such models is to first model the surface. Depending on if you want an "extruded" polymer or a cast surface will define how you restrain it. For most of my models - polymer strands of about 1000 atoms, and using about 100 strands in three layers, I restrain only the ends and only in the x direction to simulate an extrusion of a much larger molecule which is normally under stress. This lets the polymer blend in the z and y direction ( x-y surface plane ). Then proceed normally through NVT, NPT to a surface that looks and reacts as normal as an MM can do e.g. do H-bonds form in Nylon, ask if water beads on PE etc. When you feel that it is representative of the surface - add it to a library of surfaces. Then add the protein. Try to replicate https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548063/ it will get you a long way toward your goal. You can add the protein much the same way the Kalp models are shown in the tutorials.

Hope this helps
Paul
UMN , BICB

On Nov 7 2019, at 9:37 am, Sezai-Raif Baydan <sezai-raif.baydan at rwth-aachen.de> wrote:
> Hello!
>
>
>
> I am trying to simulate the adsorption of a certain peptide on a certain polymer surface. For that, I did position restrain of polymer heavy atom and position restrain of protein heavy atoms during the NVT and NPT equilibration and also during energy minimization (EM).
>
>
> The first lines of my minim.mdp file looks like this:
>
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> define = -DPOSRES -DPP_POSRES
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> constraints = none
>
>
>
> The first lines of nvt.mdp and npt.mdp looks like this:
>
>
> define = -DPOSRES -DPP_POSRES ; position restrain the protein and polymer
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 100000 ; 2 * 50000 = 200 ps
> dt = 0.002 ; 1 fs
>
>
>
> After the equilibration steps, I run my sytem for 100 ns. In my md.mdp file I just include the position restrain of polymer heavy atoms.
> I also include the position restrain files (posre.itp and posre_polym.itp) in my topology file:
>
> ; Include polymer topology
> #include "amber99sb-ildn.ff/polymer_GMX.itp"
>
> ; Include Position restraint file for polymer
> #ifdef PP_POSRES
> #include "posre_polym.itp"
> #endif
>
> ; Include water topology
> #include "./amber99sb-ildn.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "./amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> peptide and polymer in water
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Mth 225
> SOL 8621
> CL 13
>
>
>
> I do not get any gmx errors! I remove the pbc with: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc -mol -center
>
>
> When I first upload my md_0_1.gro file in VMD I can see often “artefacts”. So, a monatomic perpendicular fraction of my layer is over my peptide. And that means of course out of the box. But also in some .gro files, I can see a whole monatomic layer over the peptide! Anyway they disappear once I include my noPBC.xtc file.
>
>
> Once I load my noPBC.xtc file, I saw that the layer is not “stable”. Because when I act out the frames, I see that the layer is shifting over my peptide. It is not the whole layer which is shifting and it is not all the time but in many frames one can see these shifts. I would like to show you some screenshots about this, but the data is too big of one screenshot.
>
>
> I also try this invocation: trjconv -s md.tpr -f md.xtc -o md_noPBC_whole.xtc -pbc whole -center -ur compact
> trjconv -s md.tpr -f md_noPBC_whole -center -pbc mol
>
>
>
> But even then, I have the same problem as described before.
>
>
> When I use this: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc -mol -ur compact
>
>
> I do not see any shifting of my layer. But this time I cannot see any interactions of my peptide with the layer.
>
>
> Can somebody help me with this issue? How can I remove the pbc so I do not have any artefacts of my layer so I can see a adsorption of my peptide?
>
>
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