# Interactions between small molecules and a graphene

**URL:** <https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297>\
**Category:** User discussions\
**Tags:** forcefield, analysis-tools\
**Created:** [September 30, 2023, 12:06am UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297 "2023-09-30T00:06:59Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![HamzaALLAL](https://avatars.discourse-cdn.com/v4/letter/h/e495f1/32.png) [@HamzaALLAL](https://gromacs.bioexcel.eu/u/HamzaALLAL)\
**Post date:** [September 30, 2023, 12:06am UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297/1 "2023-09-30T00:06:59Z")

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Hello everyone,

I have an initial query regarding the feasibility of performing a molecular dynamics simulation using GROMACS.  
Specifically, I’m interested in analyzing the interactions between small molecules and a graphene surface.  
I have previously conducted multiple calculations involving ligand-protein interactions, and they have yielded successful results. However, I am now wondering if the same approach can be applied to investigate the interactions between molecules and graphene.  
Your insights and guidance on this matter would be greatly appreciated

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**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\
**Post date:** [October 1, 2023, 8:59am UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297/2 "2023-10-01T08:59:21Z")

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That can be done. There are multiple publications on this.

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**Author:** ![HamzaALLAL](https://avatars.discourse-cdn.com/v4/letter/h/e495f1/32.png) [@HamzaALLAL](https://gromacs.bioexcel.eu/u/HamzaALLAL)\
**Post date:** [October 1, 2023, 9:13am UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297/3 "2023-10-01T09:13:44Z")

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Dear rpsingh  
Can you give me links to this work or in particular links to a tutorial or something else, please.

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**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\
**Post date:** [October 14, 2023, 7:36am UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297/4 "2023-10-14T07:36:01Z")

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The setup is simple. Get a graphene molecule (use VMD, CHARMM-GUI or any other program of your choice), insert molecules using gmx insert-molecules and then solvate. Then add ions, if required, and you have the starting system. Then proceed through the usual energy minimisation, equilibration and production runs.

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<div class="post-metadata">

**Author:** ![HamzaALLAL](https://avatars.discourse-cdn.com/v4/letter/h/e495f1/32.png) [@HamzaALLAL](https://gromacs.bioexcel.eu/u/HamzaALLAL)\
**Post date:** [October 21, 2023, 4:31pm UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297/5 "2023-10-21T16:31:44Z")

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**Thank you dear rpsingh** , for the response.  
I tried but without results.  
The problem is on the preparation of the topology of the adsorbent (graphen) during the first step with gmx:  
gmx pdb2gmx -f adsorbent.pdb -o adsorbent.gro

An error appears; because my adsorbent.pdb is not a protein (also no hydrogen).

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Program gmx pdb2gmx, VERSION 5.1.5  
Source code file: /home/haz/gromacs-5.1.5/src/gromacs/gmxpreprocess/resall.c, line: 645

Fatal error:  
Residue ‘ER’ not found in residue topology database  
For more information and tips for troubleshooting, please check the GROMACS  
website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)

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<div class="post-metadata">

**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\
**Post date:** [October 29, 2023, 7:30am UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297/6 "2023-10-29T07:30:48Z")

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Don’t use pdb2gmx. CHARMM-GUI will give you gro, itp and other files of graphene that you need to run the simulation. You can directly use these files.

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<div class="post-metadata">

**Author:** ![HamzaALLAL](https://avatars.discourse-cdn.com/v4/letter/h/e495f1/32.png) [@HamzaALLAL](https://gromacs.bioexcel.eu/u/HamzaALLAL)\
**Post date:** [October 30, 2023, 7:48am UTC](https://gromacs.bioexcel.eu/t/interactions-between-small-molecules-and-a-graphene/7297/7 "2023-10-30T07:48:36Z")

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Thanks a lot,  
I’ll try.