Pbc effect removal

[alevilla]

Hi,
This topic has been addressed several times in the forum. Maybe you find the answer already in the forum using the option search.

Maybe the answer to this post can help

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…

Best regards
Alessandra