What are the terms to look forward to for proper equilibration in GROMACS?

Question

[Arindam Ghosh]

I am getting the following error while running mdrun for protein-ligand complex.

Fatal error: 6 particles communicated to PME rank 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated.

Initially I had done EM with emtol = 500 and NVT and NPT for 100ns. I had received a similar error. This time I changed emtol =100 and increased NVT, NPT time 200ns and I am still getting the same error but a bit delayed.

I had seen reports regarding similar error, where they had mentioned to remove the troubled geometry. Will this solve the problem permanently? What are the chances it will not happen again?

The mdp files I used can be found in a parallel post on Research Gate here.

Answer 1

[db4]

Any solution ? I am facing the same error. For the protein I am working on, I had to model some residues that missing in the crystal structure using: https://salilab.org/modeller/wiki/Missing%20residues. But I don't think the problem is related to that. The system can pass energy minimization but the NVT equilibration stops at the first step with the error message: "7 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated." Parameters used for energy minimization: ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization)

emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol

emstep = 0.01 ; Energy step size

nsteps = 50000 ; Maximum number of (minimization) steps to perform

energygrps = system ; Which energy group(s) to write to disk