[gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue

[Alex Cumberworth]

I am trying to simulate a system with a phosphorylated threonine residue
using Gromacs 4.5.5. I took the parameters for the TPO residue from the
gromos43a1p force field and added them to the gromos43a1 force field,
following the steps as provided on the Gromacs website. I then successfully
completed the following steps.

$bin/pdb2gmx -ignh -ff gromos43a1 -f odh.pdb -o odh.pdb -p odh.top -water
spce
$bin/editconf -bt octahedron -f odh.pdb -o odh-b4sol.pdb -d 1.0
$bin/genbox -cp odh-b4sol.pdb -cs spc216.gro -o odh-b4ion.pdb -p odh.top
$bin/grompp -f em.mdp -c odh-b4ion.pdb -p odh.top -o ion.tpr -maxwarn 5
$bin/genion -s ion.tpr -o odh-b4em.pdb -neutral -conc 0.15 -p odh.top -g
ion.log
$bin/grompp -f em.mdp -c odh-b4em.pdb -p odh.top -o em.tpr -maxwarn 5

I then tried to carry out the energy minimization (the em.mdp file is
attached)

$bin/mdrun -v -deffnm em

Only to encounter the following error

Fatal error:
6 particles communicated to PME node 4 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.

Repeating the command causes different numbers of particles to be included
in the error. I have attached a log file from mdrun. I repeated all steps
with the same protein except with a THR in place of the TPO and found no
errors. The initial structure had been minimized in CHARMM, so I downloaded
the original pdb and tested it, only to find the same error. I then tried
simulating a single TPO with the same set of steps (the editconf command
option -d 1.0 was changed to 5.0) and found the same error. I then tried
using the gromos43a1p force field more directly. I used the gromos43a1 .hdb
(and added an entry for TPO) and .atp files in place of the the ones found
in the gromos43a1p directory because of previously discussed issues with
the format. I also added the ions.itp, spce.itp, and ff_dum.itp to the
directory. However, after inputting the same commands and using the single
TPO residue, I received the same error.

Alex Cumberworth
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