PBC correction in solvent boxes

User discussions
1

GROMACS version: 2023.2
GROMACS modification: No

I want to run simulations in organic solvents so I first generated equilibrated solvent boxes. The solvent molecules in the equilibrated box are “broken“ due to PBC. I have tried PBC corrections but in vain as there are multiple molecules which are split due to PBC and not all could be wrapped. Is it OK to use these boxes with molecules split across the box (unwrapped boxes) to solvate my protein?

Thanks,

Raman

2

Hi,

you can easily test it. Just solvate your protein with your solvent box using gmx solvate. If your solvent molecules are broken in the returned structure, you will have a problem…

Why is the PBC correction not working? Remember to use a .tpr file for the “unwrapping”, e.g.,:

gmx trjconv -s solvent.tpr -f solvent.gro -pbc whole -o whole_solvent.gro

This should work, but replace my example names with the names of your files!

Best,

Marius