This might me be more of a gromacs problem but still I am posting it here. I ran a CG simulation of methanol where I have used two bead representation for each methanol molecule. I have used force-matching to generate tabulated potential. I have used almost the same grompp.mdp file as found in the methanol tutorial (I only added the groups and added constraints to the bonds). Even though I had set pbc as xyz, when I viewed my trajectory I saw many of the particles going outside the box. I am not sure why pbc is not working. I have added my cg_grompp.mdp and cg topology file.
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cg_grompp.mdp
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cgtop.top
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