Exclusions in Gromacs

User discussions
1

GROMACS version: 2022.2
GROMACS modification: No
Here post your question :

I have been trying to exclude intramolecular non-bonded interactions for a Naphthalene molecule. In [ exclusions ] section, I have included every possible atom pair to exclude within the molecule
( i.e all 18 atom indices :
[exclusions]
1 2 3 4 …18
2 1 3 4 …18
3 1 2 4 …18
.
.
.
18 1 2 …17
)
However only the LJ and dispersion forces are being excluded while the Coulomb forces are being accounted for these 18 atoms. Is there a way I can exclude them? I have tried using energy group exclusions but this functionality is not supported by the gromacs version I am using.

2

Exclusions should exclude Coulomb interactions as well. Would you be able to post all necessary input somewhere, so that it can be downloaded? I.e., if the files are not huge.

3

Thank you for the reply:

Here are all the files I think you require for diagnosis. Please let me know if you require anything further.

https://drive.google.com/drive/folders/1j82MQMDg22yvBGo35l9FOhEi0SvEGjpJ?usp=sharing