Error in CG simulation for Graphene

User discussions
1

GROMACS version:2022
GROMACS modification: Yes/No
Here post your question; I am getting the following error while trying to run this command in coarse grained simulation of graphene:
Command line:gmx_mpi grompp -f minim.mdp -c …/3pwh_memb_cg.gro -r …/3pwh_memb_cg.gro -o em.tpr -p …/topol.top
Error:Invalid line in …/system_fixed.gro for atom 1:
1GRA B1 1 6.003 6.08 8.453
How to fix this? I assume this is error is due to spacing issues.

2

It looks a bit strange:
“Command line:gmx_mpi grompp -f minim.mdp -c …/3pwh_memb_cg.gro -r …/3pwh_memb_cg.gro -o em.tpr -p …/topol.top
Error:Invalid line in …/system_fixed.gro for atom 1:”
In your command there is no system_fixed.gro file. I guess you have copied and pasted from different places, right?

Anyhow, how did you generate the system_fixed.gro file? Make sure that it adheres to the file format: File formats - GROMACS 2024.4 documentation.