# Issue with orienting two monomers during dimer insertion in GoMARTINI membrane system

**URL:** <https://gromacs.bioexcel.eu/t/issue-with-orienting-two-monomers-during-dimer-insertion-in-gomartini-membrane-system/13216>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [February 13, 2026, 3:38pm UTC](https://gromacs.bioexcel.eu/t/issue-with-orienting-two-monomers-during-dimer-insertion-in-gomartini-membrane-system/13216 "2026-02-13T15:38:56Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Rudhra](https://avatars.discourse-cdn.com/v4/letter/r/958977/32.png) [@Rudhra](https://gromacs.bioexcel.eu/u/Rudhra)\
**Post date:** [February 13, 2026, 3:38pm UTC](https://gromacs.bioexcel.eu/t/issue-with-orienting-two-monomers-during-dimer-insertion-in-gomartini-membrane-system/13216/1 "2026-02-13T15:38:56Z")

</div>

GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Hello,

I am investigating dimer formation of a membrane protein using a coarse-grained GoMARTINI model in a neuronal membrane system.

### **System setup**

· CG monomer structure: `protein_cg.gro`

· Second monomer generated using:

```auto
gmx insert-molecules -f protein_cg.gro -ci protein_cg.gro -nmol 1 -radius 4.5 -o two_monomers.gro

```

· The two-monomer system was then embedded into the membrane (attached images).

· Energy minimization, followed by NVT and NPT equilibration, was performed.

· After embedding and minimization, the COM distance between monomers was ~9 Å.

* * *

### **Issue**

After membrane embedding:

· One monomer appears properly embedded and aligned with the membrane normal.

· The second monomer is slightly tilted/rotated relative to the first.

· I am only able to translate or rotate both monomers together, not individually.

· Even after equilibration, there was no significant change in the relative orientation.

I am unsure whether:

· This slight rotational deviation is expected during membrane embedding,

· Or if it indicates improper insertion or orientation prior to embedding.

* * *

### **Questions**

1. Does `gmx insert-molecules` introduce random rotational orientations for inserted molecules?

2. If so, what is the recommended workflow to ensure two monomers have identical orientation before membrane embedding?

3. Is ~9 Å COM separation too close for an unbiased dimerization study in MARTINI CG simulations?

4. If the system remains stable during equilibration, can this orientation difference be considered acceptable?

I would be grateful for any advice or recommendations regarding best practices for preparing a controlled dimer setup in membrane coarse-grained simulations.

Thank you

 ![Screenshot from 2026-02-12 00-50-17](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c98d3aac785c31f456b46464b1f4d02bd3360c54.jpeg)

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