[gmx-users] 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group

Justin A. Lemkul jalemkul at vt.edu
Fri May 14 20:03:09 CEST 2010



Joanne Martin wrote:
> Hi im trying to run an NVT equilibration, and im getting the following 
> errors
> these are my commands for solvating the box...........
> any suggestions would be greatly appreciated
> J
> 

Did you search the Gromacs website and/or mailing list archive?

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

-Justin

> editconf -f 2VVSET_complex.gro -o 2VVSET_complex_conf.gro -box 12
> genbox -cp 2VVSET_complex_conf.gro -cs 
> /programs/gromacs-4.0.4/share/gromacs/top/ffamber_tip3p -o 
> 2VVSET_complex_SOL.gro -p 2VVS_complex.top
> 
> output
>  
> starting mdrun 'Protein in water'
> 200000 steps,    400.0 ps.
> Warning: 1-4 interaction between 4346 and 4350 at distance 3.066 which 
> is larger than the 1-4 table size 1.900 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> MPI Application rank 19 killed before MPI_Finalize() with signal 11
> MPI Application rank 17 killed before MPI_Finalize() with signal 11
> 
> -------------------------------------------------------
> Program mdrun_mpi4.0.4, VERSION 4.0.4
> Source code file: pme.c, line: 518
> 
> Fatal error:
> 3 particles communicated to PME node 7 are more than a cell length out 
> of the domain decomposition cell of their charge group
> 

-- 
========================================

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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