How to solve error of 498 particles communicated to PME rank 5 are more than 2/3 times the cut-off?

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1

GROMACS version:2020
GROMACS modification: Yes/No Yes
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Dear gromacs users
I am doing a protein-ligand simulation for which I did minimization and nvt equilibration which did not give any warning. However, at the start of npt equilibration, I am getting the following error:-
498 particles communicated to PME rank 5 are more than 2/3 times the cut-off
out of the domain decomposition cell
My output for energy minimization and nvt are as below:-
Steepest Descents converged to Fmax < 1000 in 1600 steps
Potential Energy = -2.1638772e+06
Maximum force = 9.9330219e+02 on atom 5358
Norm of force = 1.2163581e+01

nvt output
Statistics over 50001 steps using 501 frames

Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
6.20748e+03 1.66903e+04 2.10384e+04 9.80651e+02 7.90629e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Position Rest.
7.25355e+04 2.44361e+05 -2.16657e+06 6.94831e+03 2.20227e+03
Potential Kinetic En. Total Energy Conserved En. Temperature
-1.78770e+06 3.47505e+05 -1.44020e+06 -1.81078e+06 2.97636e+02
Pressure (bar) Constr. rmsd
-6.60718e+02 0.00000e+00

Total Virial (kJ/mol)
1.44902e+05 1.77751e+02 -1.92717e+02
1.79569e+02 1.45008e+05 4.25309e+02
-1.91979e+02 4.20789e+02 1.44706e+05

Pressure (bar)
-6.62397e+02 -4.49993e+00 3.54963e+00
-4.54129e+00 -6.62686e+02 -9.51883e+00
3.53285e+00 -9.41599e+00 -6.57069e+02

T-Protein_NAP_NAS_G6PT-Water_and_ions
2.97752e+02 2.97627e+02

How should I solve this problem? I need your suggestions. Please find the npt.mdp file attached.
npt.mdp (2.6 KB) npt.mdp (2.6 KB)

2

Is the simulation stable without the ligands?

3

Dear Justin
I submitted simulation same simulation with ligands using 8 cores on a local system and it worked without any error which was giving error on 32 cores. However when I try to extend it after 1ns it gives same error. Running simulation without ligand workked well without an error.
Please guide me to sort this problem.
Thanks.
Sadaf

4

I really don’t have a good idea, but perhaps your system is very fragile and experiences large changes in system volume/DD cell size, leading to numerical instability.