[gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

[Justin A. Lemkul]

ajani haresh wrote:
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> Respected Sir,
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> Myself Haresh  Ajani from National Institute of Pharmaceutical Education 
> & Research.
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> I am using gromacs version 4.5.3. I am working on molded Protein.
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> I am facing one problem in gromacs after minimization of the protein.
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> I have put my query here.
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> Fatal Error : Wrote pdb files with previous and current coordinates
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> Warning: 1-4 interaction between 687 and 691 at distance 4.001 which is 
> larger than the 1-4 table size 2.000 nm
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> These are ignored for the rest of the simulation
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> This usually means your system is exploding,
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> if not, you should increase table-extension in your mdp file
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> or with user tables increase the table size
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> Fatal error:
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> 9 particles communicated to PME node 5 are more than 2/3 times the 
> cut-off out of the domain decomposition cell of their charge group in 
> dimension x.
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> This usually means that your system is not well equilibrated.
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> I have given run for gromacs.
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> Pdb2gmx -f 1.pdb -o 12.pdb -p 12.top -ignh -ter -missing
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> then I have selected gromos force field and SPC water model.
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> editconf -bt cubic -f 12.pdb -o 123.pdb -c -d 0.9
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> genbox -cp 123.pdb -cs spc216.gro -p 123.top -o 123_b4ion.pdb
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>  then neutralize the protein and  energy minimization.
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> Steepest Descents:
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>    Tolerance (Fmax)   =  1.00000e+03
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>    Number of steps    =         3500
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> writing lowest energy coordinates.
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> Steepest Descents converged to Fmax < 1000 in 3468 steps
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> Potential Energy  = -9.6223600e+05
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> Maximum force     =  9.3264703e+02 on atom 695
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> Norm of force     =  2.5498827e+01
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> Step 0, time 0 (ps)  LINCS WARNING
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The outcome of energy minimization seems reasonable, but the fact that the 
system instantly explodes suggests that there is still something physically 
unreasonable in (1) your .mdp file or (2) the coordinates of the system.

http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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