[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
alexandercumberworth at gmail.com
Wed Jun 6 02:58:45 CEST 2012
I apologize to anyone who wasted their time reading my original post: I
found that integrator had been misspelt in the em.mdp file, causing it to
default to integrator = md. After fixing the mistake, no more errors
On Tue, Jun 5, 2012 at 4:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> On 6/5/12 7:36 PM, Alex Cumberworth wrote:
>> I am trying to simulate a system with a phosphorylated threonine residue
>> Gromacs 4.5.5. I took the parameters for the TPO residue from the
>> 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
>> $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
>> $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
>> $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.
> The message in the log file attached and printed here are not from EM,
> they are from MD. What was the outcome of EM? What were the values of
> Fmax and Epot? The log file appears to be running MD in the absence of any
> temperature coupling and other necessary parameters for proper
> equilibration, unless you are trying NVE, but the settings are also not
> correct for NVE, either.
> Better minimization and/or proper settings for equilibration should
> alleviate the issue.
> 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.
>> 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
>> 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
>> 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
>> commands and using the single TPO residue, I received the same error.
>> Alex Cumberworth
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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