# Regarding comm\_grps in mdp files for Membrane protein simulation

**URL:** <https://gromacs.bioexcel.eu/t/regarding-comm-grps-in-mdp-files-for-membrane-protein-simulation/11799>\
**Category:** User discussions\
**Created:** [March 25, 2025, 3:32am UTC](https://gromacs.bioexcel.eu/t/regarding-comm-grps-in-mdp-files-for-membrane-protein-simulation/11799 "2025-03-25T03:32:21Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Ligand1](https://avatars.discourse-cdn.com/v4/letter/l/278dde/32.png) [@Ligand1](https://gromacs.bioexcel.eu/u/Ligand1)\
**Post date:** [March 25, 2025, 3:32am UTC](https://gromacs.bioexcel.eu/t/regarding-comm-grps-in-mdp-files-for-membrane-protein-simulation/11799/1 "2025-03-25T03:32:21Z")

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GROMACS version:2022.5  
GROMACS modification: No

Hi, I am doing a membrane protein simulation based on the system prepared using CHARMM GUI. I was going through one of the equilibration.mdp files and came across a question. The mdp file has tc\_grps = SOLU MEMB SOLV (SOLU (protein) and Membrane grouped separately) and comm\_grps = SOLU\_MEMB SOLV (Protein and Membrane grouped together). This is little confusing since for tc\_grps also it should be SOLU\_MEMB and SOLV just like the comm\_grps. Infact the Membrane Protein: KALP15 in DPPC tutorial written by Dr. Lemkul also describes the same thing. Can some expert please help me with this question.

Thanks in advance

Best regards

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<div class="post-metadata">

**Author:** ![Ligand1](https://avatars.discourse-cdn.com/v4/letter/l/278dde/32.png) [@Ligand1](https://gromacs.bioexcel.eu/u/Ligand1)\
**Post date:** [March 25, 2025, 5:24pm UTC](https://gromacs.bioexcel.eu/t/regarding-comm-grps-in-mdp-files-for-membrane-protein-simulation/11799/2 "2025-03-25T17:24:06Z")

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Can some one answer this query please

Thanks in advance

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [March 27, 2025, 7:26am UTC](https://gromacs.bioexcel.eu/t/regarding-comm-grps-in-mdp-files-for-membrane-protein-simulation/11799/3 "2025-03-27T07:26:58Z")

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Nowadays one can in nearly all cases uses a single group for both temperature coupling and center of mass removal. Multiple groups is a remnant for old times when integration was not sufficiently accurate.

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<div class="post-metadata">

**Author:** ![Ligand1](https://avatars.discourse-cdn.com/v4/letter/l/278dde/32.png) [@Ligand1](https://gromacs.bioexcel.eu/u/Ligand1)\
**Post date:** [March 28, 2025, 1:56am UTC](https://gromacs.bioexcel.eu/t/regarding-comm-grps-in-mdp-files-for-membrane-protein-simulation/11799/4 "2025-03-28T01:56:13Z")

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Hi Dr. Hess,

Many thanks answering my question. So if I understand correctly, I can have tc\_grps = SOLU\_MEMB\_SOLV and comm\_grps = SOLU\_MEMB\_SOLV.

Also, I have a follow-up question. I already ran the simulations with coupling protein and membrane separately and water and ions separately as shown below:  
tc\_grps = SOLU\_MEMB SOLV and comm\_grps = SOLU\_MEMB SOLV

Is this approach still accurate.

Thanks for answering my question

best regards

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [March 28, 2025, 9:27am UTC](https://gromacs.bioexcel.eu/t/regarding-comm-grps-in-mdp-files-for-membrane-protein-simulation/11799/5 "2025-03-28T09:27:09Z")

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I suggest to use “system”, as then you are sure you are not excluding any atoms.