GROMACS version: 2022.3
Hi,
I am running an absolute FEP on a protein-ligand complex on GROMACS 2022.3 version.
I have received the following erorr during energy minimization as well as NVT equilibration.
“Fatal error:
There are perturbed non-bonded pair interactions beyond the pair-list cutoff
of 1.007 nm, 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.”
I read through the discussion forum and many suggested to keep couple-intramol=yes for large molecules. I did that but the error still seems to occur.
I have attached the MDP file and the topol file.
Any suggestions will be appreciated :)
Thanking you in advance.
Regards,
Kandwal
enmin.mdp (3.2 KB)
nvt.mdp (4.6 KB)
topol.top (434.0 KB)
I would suggest first energy minimizing and equilibrating in fully interacting bound state (if you’ve got those coordinates). After that you can chain a set of further equilibrations in the lambda states:
0 → 1 → 2 → 3 → 4 → 5 etc
That is usually the most efficient way to do it.
If you don’t have the coordinates of the bound state it will be more challenging, but then I would suggest that you energy minimize and equilibrate your protein structure, then you can insert your energy-minimized ligand in the binding site, in a reasonable conformation. And then run the equilibration sequence:
29 → 28 → 27 → 26 → 25 etc
Hi @MagnusL,
Thank you so much for the suggestion. I tried as you had mentioned i.e., to first energy minimize and equilibrate in fully interacting bound state but the erorr still seems to appear. After this, the energy minimisation step ran fine for the spcified lambdas but it failed for NVT equilibration with the following error
“Fatal error:
There are perturbed non-bonded pair interactions beyond the pair-list cutoff
of 1.011 nm, 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.”
Is this a common error that appears while running AFEP? I have observed the same error for different protein-ligand systems.
Best regards,
Kandwal
In many cases this error is related to alchemical FEP simulations, yes, especially if couple-intramol = no, which it isn’t in your case. In this case I would think that the system is not stable. Depending on how the input configuration was generated, you might have to run a long equilibration (possibly with suitable restraints on the ligand and protein backbone) before it makes sense to consider alchemical free energy calculations.
Does the error go away if you run the EM and NVT without alchemical FEP? If so, then it might be stable if you start your first alchemical FEP equilibration (in fully decoupled state, assuming that’s how the system was equilibrated) from that NVT equilibration.