GROMACS version: 2024.2
GROMACS modification: No
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Hi
I’m trying to run a coarse-grained simulation of a nanoparticle and a bilayer. The nanoparticle has a hollow shell so the beads that compose the shell are bonded together with a spring constant in the ITP file. Neighboring beads were bonded using a cut-off distance of 1.24 nm. However, the non-bonded interactions use a 1.1 nm cut-off.
When I use gmx grompp with an equilibrated system, I get the following error message for atoms 145 and 153 which are nearest neighbors:
The largest distance between excluded atoms is 1.154 nm between atom 145 and 153, which is larger than the cut-off distance. This will lead to missing long-range corrections in the forces and energies.
I’ve run the same system with the 2021.5 version without any issues.
How to reproduce the issue with these files:
gmx grompp -f mdp.mdp -c init.gro -p topology.top -n index.ndx -o tpr
Any help is appreciated,
Carlos