Fixing periodic boundary conditions distance artefacts

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Seemingly unresolvable PBC problem on protein complex

GROMACS version: 2019.4 GROMACS modification: No Dear All, I have a protein complex on which I ran some REMD and I want to solve PBC issues before analysis. However, no matter what I tried, one of the proteins still jumps out of the box. Firstly I make the system whole with: $gmx trjconv -f md.xtc -s nvt_298.15.tpr -pbc whole -o whole -n index.ndx This makes the molecules whole, although both proteins in the complex “jump around”. I have then centered the system on an interfacial residue…

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