How to replicate the simulation box (input: gro/pdb file) with PBC?

User discussions
1

GROMACS version: 2022.5
GROMACS modification: Yes/No
I have a gro/pdb file of a membrane bilayer which is periodic. How do I replicate/repeat the box in x/y/z direction?

2

When simulating? Use the default pbc = xyz setting in the mdp file.
If you want to see the periodic images when you visualize the system, it will be different from one program to another. In VMD you can use the options in Graphics->Representations… Look for the Periodic tab and you can set the representation you would like.

3

Thanks for the reply.
I meant, before simulation. I want to replicate the atoms in the pdb/gro file and save it as a new pdb.
Can that be done in GROMACS, using any command (like editconf)?
I tried VMD, but not able to save the coordinates as a new pdb.

4

I see. Try gmx genconf - GROMACS 2024.4 documentation.

5

Thank you. It works.