# Comm-mode with position restraints

**URL:** <https://gromacs.bioexcel.eu/t/comm-mode-with-position-restraints/3076>\
**Category:** User discussions\
**Created:** [November 4, 2021, 6:20am UTC](https://gromacs.bioexcel.eu/t/comm-mode-with-position-restraints/3076 "2021-11-04T06:20:34Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![tejchoksi](https://avatars.discourse-cdn.com/v4/letter/t/e56c9b/32.png) [@tejchoksi](https://gromacs.bioexcel.eu/u/tejchoksi)\
**Post date:** [November 4, 2021, 6:20am UTC](https://gromacs.bioexcel.eu/t/comm-mode-with-position-restraints/3076/1 "2021-11-04T06:20:35Z")

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GROMACS version: 2020.5  
GROMACS modification: No

Hi Everyone,

My systems contains a mineral slab with water above it. I am applying position restraints to the mineral slab.

I came across this note: “Removing center of mass motion in the presence of position restraints might cause artifacts. When you are using position restraints to equilibrate a macro-molecule, the artifacts are usually negligible.”

So, would you advise that I set comm-mode to None? Or should I set comm-mode to linear, with comm-grps = everything that’s not being position restrained?

Thank you for your help!

Sincerely,

Tej S. Choksi

Assistant Professor  
School of Chemical and Biomedical Engineering  
Nanyang Technological University, Singapore  
Block N1.2, B1-18, 62 Nanyang Drive  
Singapore 637459, Office: +65 6316 8940

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [November 5, 2021, 8:33am UTC](https://gromacs.bioexcel.eu/t/comm-mode-with-position-restraints/3076/2 "2021-11-05T08:33:48Z")

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Hi,

it depend on the kind of simulation you intend to carry out.

I usually set `comm-mode` to `None` every time I have restrained molecules, even for equilibration runs, but this is very specific to my system (I have an interface that need to relax, so there is some non-negligible mass flow that could be hindered if com motion is removed).

I am not sure setting `comm-mode` to `linear`, with `comm-grps = everything` that’s not being position restrained would help; assume that you start with a not-so-equilibrated box where water still doesn’t have the correct density: in this case the com of the water group would possibly get closer or farther from the restrained mineral substrate after equilibration, if `comm-mode` is set to `None`. On the other hand, if you remove com motion you may end up either (a) having an incorrect liquid density or (b) having incorrect liquid layering close to the substrare or (c) slowing down thw equilibration run (or maybe (a), (b) and (c), hard to tell). Does it make sense?