# Coarse-grained md simulatioin

**URL:** <https://gromacs.bioexcel.eu/t/coarse-grained-md-simulatioin/8590>\
**Category:** User discussions\
**Tags:** forcefield, analysis-tools, simulation-setup\
**Created:** [March 12, 2024, 12:36pm UTC](https://gromacs.bioexcel.eu/t/coarse-grained-md-simulatioin/8590 "2024-03-12T12:36:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Baibhabshri](https://avatars.discourse-cdn.com/v4/letter/b/e47774/32.png) [@Baibhabshri](https://gromacs.bioexcel.eu/u/Baibhabshri)\
**Post date:** [March 12, 2024, 12:36pm UTC](https://gromacs.bioexcel.eu/t/coarse-grained-md-simulatioin/8590/1 "2024-03-12T12:36:18Z")

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GROMACS version: 2021.4  
GROMACS modification: No  
I have a doubt for coarse grained md simulation. I have used martinize.py script to model the protein. But from here I do not understand on what basis it modelled the protein. There are 2 chain in the protein, So, it split chain A in 5 chains, 1: 3 atoms in 1 residue,2: 278 atoms in 35 residue, 3: 6 atoms in 2 residues, 3:278 atoms in 35 residues, 5: 3 atoms in 1 residues. and for chain B, 1060 atoms in 130 residues. Suppose I want to form residue wise beads with martini. Is it possible?

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**Author:** ![Marius](https://avatars.discourse-cdn.com/v4/letter/m/ed655f/32.png) [@Marius](https://gromacs.bioexcel.eu/u/Marius)\
**Post date:** [March 13, 2024, 2:59pm UTC](https://gromacs.bioexcel.eu/t/coarse-grained-md-simulatioin/8590/2 "2024-03-13T14:59:47Z")

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Hi @Baibhabshri ,

This seems not be a GROMACS related problem. You may want to take a look at the MARTINI forum/website: [http://www.cgmartini.nl](http://www.cgmartini.nl). (They also provide a lot of detailed tutorials about setting up a system with MARTINI using GROMACS!)

Quick answer for the coarse graining approach in MARTINI: MARTINI merges usually 4 heavy atoms (e.g. 4 C-Atoms) to one MARTINI bead. The mapping is fixed for most standard residues like amino acids or lipids.

Hope that helped.

All the best,  
Marius

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**Author:** ![Baibhabshri](https://avatars.discourse-cdn.com/v4/letter/b/e47774/32.png) [@Baibhabshri](https://gromacs.bioexcel.eu/u/Baibhabshri)\
**Post date:** [March 14, 2024, 5:52am UTC](https://gromacs.bioexcel.eu/t/coarse-grained-md-simulatioin/8590/3 "2024-03-14T05:52:18Z")

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But what I saw that, there were 130 residue and 1060 atoms in one chain, if that converted that in 130 beads is not it like it is residue wise bead formation?