Severe artifacts with PME during free energy calculations

User discussions
1

GROMACS version: 2019
GROMACS modification: No

Dear all,

I am calculating the free energy of solvation for the cofactor in the protein. I do the very same thing as in the gromacs tutorial for Methane in Water.

I run md trajectories for several intermediate states (lambda). The trajectories with integral charge (i.e. for the charge=1, and for the charge=0 with varying vdw parameters) are ok.

All the other trajectories with cofactor q = 0.875, 0.75, …, 0.125 crash with the following mistake:

WARNING: Listed nonbonded interaction between particles 4197 and 4207
at distance 47.559 which is larger than the table limit 2.200 nm.

I do not know how this could happen, it looks like the PME artifact, because the distance is ok, and the system did not blow up.

Maybe I should insert some modifications in the .mdp parameters?

Thank you in advance,
Dmitrii

2

This topic looks blurred in my list in the “Latest”. Can it be seen by anyone?

3

It looks like you’re trying to transform a relatively large molecule. A more complete description and full .mdp parameters (at least the free energy section) would be helpful. But depending on whether you’re coupling intramolecular interactions, that can trigger the creation of all-vs-all intramolecular exclusions, which can extend over great distance, depending on the geometry of the system, therefore severely restricting how you can parallelize the system.

4

Thank you! I could finally fix the problem