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

**URL:** <https://gromacs.bioexcel.eu/t/how-to-replicate-the-simulation-box-input-gro-pdb-file-with-pbc/10537>\
**Category:** User discussions\
**Created:** [November 13, 2024, 9:29am UTC](https://gromacs.bioexcel.eu/t/how-to-replicate-the-simulation-box-input-gro-pdb-file-with-pbc/10537 "2024-11-13T09:29:06Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![vardhan](https://avatars.discourse-cdn.com/v4/letter/v/ebca7d/32.png) [@vardhan](https://gromacs.bioexcel.eu/u/vardhan)\
**Post date:** [November 13, 2024, 9:29am UTC](https://gromacs.bioexcel.eu/t/how-to-replicate-the-simulation-box-input-gro-pdb-file-with-pbc/10537/1 "2024-11-13T09:29:06Z")

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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?

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 13, 2024, 10:09am UTC](https://gromacs.bioexcel.eu/t/how-to-replicate-the-simulation-box-input-gro-pdb-file-with-pbc/10537/2 "2024-11-13T10:09:09Z")

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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.

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**Author:** ![vardhan](https://avatars.discourse-cdn.com/v4/letter/v/ebca7d/32.png) [@vardhan](https://gromacs.bioexcel.eu/u/vardhan)\
**Post date:** [November 13, 2024, 10:45am UTC](https://gromacs.bioexcel.eu/t/how-to-replicate-the-simulation-box-input-gro-pdb-file-with-pbc/10537/3 "2024-11-13T10:45:20Z")

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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.

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 13, 2024, 11:00am UTC](https://gromacs.bioexcel.eu/t/how-to-replicate-the-simulation-box-input-gro-pdb-file-with-pbc/10537/4 "2024-11-13T11:00:29Z")

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I see. Try [gmx genconf - GROMACS 2024.4 documentation](https://manual.gromacs.org/current/onlinehelp/gmx-genconf.html).

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**Author:** ![vardhan](https://avatars.discourse-cdn.com/v4/letter/v/ebca7d/32.png) [@vardhan](https://gromacs.bioexcel.eu/u/vardhan)\
**Post date:** [November 14, 2024, 11:32am UTC](https://gromacs.bioexcel.eu/t/how-to-replicate-the-simulation-box-input-gro-pdb-file-with-pbc/10537/5 "2024-11-14T11:32:40Z")

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Thank you. It works.