Question: What are the terms to look forward to for proper equilibration in GROMACS?
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gravatar for Arindam Ghosh
20 months ago by
Arindam Ghosh180
India
Arindam Ghosh180 wrote:

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.

molecular dynamics gromacs • 857 views
ADD COMMENTlink modified 11 months ago by db410 • written 20 months ago by Arindam Ghosh180
0
gravatar for db4
11 months ago by
db410
db410 wrote:

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

ADD COMMENTlink modified 11 months ago • written 11 months ago by db410
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