# Multimer simulation
**URL:** https://gromacs.bioexcel.eu/t/multimer-simulation/10352
**Category:** User discussions
**Tags:** pdb2gmx
**Created:** [October 16, 2024, 10:00am UTC](https://gromacs.bioexcel.eu/t/multimer-simulation/10352 "2024-10-16T10:00:17Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Vini161](https://gromacs.bioexcel.eu/u/Vini161)
#### Post date: [October 16, 2024, 10:00am UTC](https://gromacs.bioexcel.eu/t/multimer-simulation/10352/1 "2024-10-16T10:00:17Z")
GROMACS version: 2021
GROMACS modification: No
I am running. multimer simulation, especially dimer and hexamer (2 and 6 chains). I am using lysozyme in water tutorial but during pdb to gmx it takes the whole protein dimer to be a single chain in gro (the structure is conserved) such that i have to retrive the structure and rename chains manually in pymol, any insight is appreciated?
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### Author:  [@davide.messina](https://gromacs.bioexcel.eu/u/davide.messina)
#### Post date: [October 20, 2024, 11:22am UTC](https://gromacs.bioexcel.eu/t/multimer-simulation/10352/2 "2024-10-20T11:22:19Z")
Good day,
I would look at the .pdb file: if it has the chain ID, GROMACS will assign it.
Then, you may want to index those groups/chains by using
gmx make\_ndx -f your\_input.pdb -o index.ndx
using “chain A” etc. to save new groups with your chain
another way (if you know the residues of chain A, example from 1 to 200 etc…) is to create an index group using your \*.gro file:
call gmx make\_ndx and enter in the interactive shell “r 1-200”, then you can change the name
Hope this helps!