# Simulation of small molecule in lipid bilayer

**URL:** <https://gromacs.bioexcel.eu/t/simulation-of-small-molecule-in-lipid-bilayer/1400>\
**Category:** User discussions\
**Created:** [January 7, 2021, 12:17pm UTC](https://gromacs.bioexcel.eu/t/simulation-of-small-molecule-in-lipid-bilayer/1400 "2021-01-07T12:17:46Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![drrahulsuresh](https://avatars.discourse-cdn.com/v4/letter/d/e68b1a/32.png) [@drrahulsuresh](https://gromacs.bioexcel.eu/u/drrahulsuresh)\
**Post date:** [January 7, 2021, 12:17pm UTC](https://gromacs.bioexcel.eu/t/simulation-of-small-molecule-in-lipid-bilayer/1400/1 "2021-01-07T12:17:46Z")

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Hi users,  
I have a doubt regarding the simulation of small molecule in bilayer system. The bilayer system is generated using charmm gui. The small molecule need to be placed in water, on the surface of bilayer.  
The ligand is polyene structure.  
Is there any method by which I can insert the molecule into the system.  
The insert molecule command doesn’t work du to the absence of solvation box. So I tried creating a solvation box using “gmx editconf -f ligand.pdb -ci lipid.gro -o output.gro -bt cubic -d 1.0”  
But the insert molecule command ends up with error, undefined solute box. I tried adding the solute box explicitly using -box flag to editconf, but the error prevails.  
Any suggestions on how to perform this simulation?

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [January 12, 2021, 1:51pm UTC](https://gromacs.bioexcel.eu/t/simulation-of-small-molecule-in-lipid-bilayer/1400/2 "2021-01-12T13:51:00Z")

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Hi,  
did you try gmx insert-molecules [gmx insert-molecules — GROMACS 2020.5 documentation](https://manual.gromacs.org/current/onlinehelp/gmx-insert-molecules.html) with the option -ip?  
Best regards  
Alessandra

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**Author:** ![drrahulsuresh](https://avatars.discourse-cdn.com/v4/letter/d/e68b1a/32.png) [@drrahulsuresh](https://gromacs.bioexcel.eu/u/drrahulsuresh)\
**Post date:** [January 12, 2021, 4:04pm UTC](https://gromacs.bioexcel.eu/t/simulation-of-small-molecule-in-lipid-bilayer/1400/3 "2021-01-12T16:04:36Z")

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Hi.  
Thanks for the reply.  
Insert molecule was more complicated for me. The I used charmm gui which was able to generate the complex system.

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**Author:** ![Karukuvelraja](https://avatars.discourse-cdn.com/v4/letter/k/dfb087/32.png) [@Karukuvelraja](https://gromacs.bioexcel.eu/u/Karukuvelraja)\
**Post date:** [October 1, 2024, 5:19am UTC](https://gromacs.bioexcel.eu/t/simulation-of-small-molecule-in-lipid-bilayer/1400/4 "2024-10-01T05:19:20Z")

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How you generate membrane bilayer with ligand