Energy minimization has stopped!

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1

GROMACS version:2022.3
GROMACS modification: Yes/No
Hi!

During the energy minimization of 3 100mer (4500 atoms) in a box the following note appeared:

Energy minimization has stopped because the force on at least one atom is not
finite. This usually means atoms are overlapping. Modify the input
coordinates to remove atom overlap or use soft-core potentials with the free
energy code to avoid infinite forces.
You could also be lucky that switching to double precision is sufficient to
obtain finite forces.

(I also have checked the starting structure.)

It would be a great help if anybody could guide me to fix that.

2

Something about the system is impossible, either the coordinates, the force field parameters being used, topology (connectivity), etc. The error tells you that atoms are overlapping, which suggests the topology is not sound, but it’s hard to say without more information like what your system is, how you generated and validated its topology, etc.

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