The largest distance between excluded atoms is 1.725 nm, which is larger than the cut-off distance

PSS67
Wed, 11 May 2022 15:12:43 +0000
User discussions

GROMACS version: 2022.1
GROMACS modification: No
When using editconf to make a box from a crystal lattice (4x4x4 unit cells) and using a gro file which is fine, I get a new gro file where there are some bad H-H interactions. Moreover, when I try to run grompp in order to do an energy minimization, I get the error:
The largest distance between excluded atoms is 1.725 nm, which is larger than the cut-off distance. This will lead to missing long-range corrections in the forces and energies.
I have never encountered this error before and I am wondering what has caused it. I am using a cut-off distance of 1.0 which I can’t increase without also increasing the box, but I don’t think that this is the problem. Any help would be appreciated, Thanks, Peter

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