[gmx-users] distance/bonds restrains in gromacs2016.3 with domain decomposition

[Yulian Gavrilov]

Dear all,

I try to restrain the conformation of a protein using distance/bonds
restrains.
I have a problem when I try to use distance restraints or restraint
potential (bonds type 10) together with domain decomposition.

I use gromacs2016.3. It seems that this issue should be solved for 2016
version:
http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/release-notes.html
[Made distance restraints work with threads and DD]

However, I get an error (both for bonds and distance restraints):

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given
box and a minimum cell size of 9.15291 nm
Change the number of ranks or mdrun option -rdd or -dds [this does not help]
Look in the log file for details on the domain decomposition



My steps:

1. Add to .top file:

[ bonds ]
; ai   aj   type    low     up1     up2     kdr
  43   87     10    0.28     0.31    0.33     1000
  53  107     10    0.28     0.31    0.33     1000
...

or

[ distance_restraints ]
; ai   aj   type   index   type'      low     up1     up2     fac
  43   87      1       0       1      0.28    0.31    0.33    1.0
  53  107      1       0       1      0.28    0.31    0.33    1.0
...

in case of  [ distance_restraints ] I add to mdp file:
disre           = simple; simple or ensemble
;nstdisreout=0
disre-fc        = 1000; [kJ mol^-1 nm^-2]

2. Run it with this script:

#PBS -q sleep -l select=8:ncpus=8:mem=5000mb
...
echo Using modules `module list`
setenv OMP_NUM_THREADS 8
...
module load mkl/11.3.4.258  gcc/4.9.3  impi/5.1.3.258
source /usr/local/gromacs-2016.3/bin/GMXRC.csh
...
mpirun gmx_mpi mdrun -v -deffnm md100ns


Please can you suggest something or explain what I am doing wrong?



-- 
Sincerely,
Yulian Gavrilov