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
That can be done. There are multiple publications on this.
Dear rpsingh
Can you give me links to this work or in particular links to a tutorial or something else, please.
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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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).
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
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.