Fix PBC effects

["ROPÓN-PALACIOS G."]

Dear All,

I have my protein+membrane+ligand system (as you can see in the attached figure) as a result of 500 ns of simulation with the charmm-gui protocol, but I don't know how to remove the PBC effects, it's the first time I've had a problem I have tried to correct this, but I can't find a solution, I don't know if you could help me with this.

Thanks.

[Hugo Macdermott-Opeskin]

Hi, 

What simulation software was your simulation run in? Generally it is easiest to fix your PBCs using a simulation postprocessing tool such as gmx trjconv from GROMACS rather than in MDAnalysis.  I will note that your box looks rather square but that your membrane + protein + ligand seems sprayed everywhere. Are you sure this is only a PBC issue?

Cheers