[gmx-users] Fwd: Problem in applying walls in the z direction

[Stephen Chan]

Dear all,

I'm running a simulation of a bilayer system and I would like to apply 
wall condition to both xy planes (i.e. nwall = 2). On top of the normal 
MD settings, I added a couple of lines to the mdp file:
pbc             = xy
nwall           = 2
wall-type       = 10-4
wall-density    = 5  5
wall-atomtype   = OT OT
ewald-geometry  = 3dc

integrator              = md
dt                      = 0.002
nsteps                  = 50000000
nstlog                  = 10000
nstxout                 = 0
nstvout                 = 0
nstfout                 = 0
nstcalcenergy           = 10000
nstenergy               = 10000
nstxout-compressed      = 10000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.0
coulombtype             = pme
rcoulomb                = 1.0
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 0.9
rvdw                    = 1.0
;
tcoupl                  = Nose-Hoover
tc_grps                 = PROT   MEMB   SOL_ION
tau_t                   = 1.0    1.0    1.0
ref_t                   = 310 310 310
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0
compressibility         = 0.0     4.5e-5
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = PROT   MEMB   SOL_ION
;
refcoord_scaling        = com

When running grompp, I managed to generate the tpr file from my input
gro file. However, when running mdrun, I got the following error:

Fatal error:
There is no domain decomposition for 84 ranks that is compatible with
the given box and a minimum cell size of 14.9422 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

Any help would be appreciated :)

Best regards,

Stephen