normal Protein System tends to collapse while using Martini 3

  • mkarroum
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8 months 2 weeks ago #9700 by mkarroum
My system includes a tetramer protein composed of four monomers and a peptide binding to it. Initially, I conducted a Coarse-Grained simulation using the Martini 2 force field after setting up my system through charmm-gui, utilizing the elnedyn22 model. The simulation concluded successfully, yielding the anticipated results.

Then, I attempted a new simulation, this time employing the Martini 3.0.0 model instead of elnedyn22, and I faithfully followed the same procedures in charmm-gui for system preparation. However, the results from this simulation were markedly different. The tetramer protein's structure, consisting of the four monomers, exhibited a tendency to collapse. This meant that the tetramer structure became disrupted, with each monomer deviating significantly from the others. I also investigated the possibility of periodic boundary conditions (PBC) causing this error but found no evidence to support that.

I'm wondering what might be the root cause of these errors? Thanks in advance.

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8 months 2 weeks ago - 8 months 2 weeks ago #9701 by bart
I am not sure if you added elastic bonds between the monomers when you were using elnedyn22, if you did, that explains for sure why it cannot fall apart.

In Martini3 you can use elastic networks or Go bonds. Go bonds can break, so the complex can fall apart. However, the structure of the monomers should be very well preserved.

In short it is not completely clear to me what has been done and what is expected of the answer.
Last edit: 8 months 2 weeks ago by bart. Reason: typos

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