Error during energy minimization

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1

GROMACS version: 2025.0
GROMACS modification: No
pmx version: 0+untagged.888.g09b57c6

Hello,
I’m currently trying to setup and perform ABFE calculations using GROMACS and PMX. During energy minimization for lambda=0 (same error for lambda=1) I got error:

Fatal error:
There are 2 perturbed, excluded non-bonded pair interactions beyond the
pair-list cut-off, which is not supported. This can happen because the system
is unstable or because intra-molecular interactions at long distances are
excluded. If the latter is the case, you can try to increase nstlist or rlist
to avoid this.The error is likely triggered by the use of couple-intramol=no
and the maximal distance in the decoupled molecule exceeding rlist.

How can I solve this error?
nstlist/rlist increase doesn’t help.
Attached mdp file and topology.
I can attach link to coordinates file if it helps with google drive.

em_l0.mdp (7.6 KB)
ligand.top (24.2 KB)

2

Use couple-intramol=yes and add a vacuum leg to your calculation. If the maximum distance is close to rlist you can consider increasing rlist instead.

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3

Thanks for your answer. Could you please describe what do you mean by “vacuum leg”? As far as I know vacuum simulations currently not supported in GROMACS.

4

You need to compute the cost of (de)coupling the molecule in vacuum. You remove the solvent from the system, keep the same box and run exactly the same calculations as for the solvent case.

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5

Thank you!