[gmx-users] question_gromacs

[Andrew Bostick]

Dear Gromacs users

I have following error when I do equilibration:

There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 0.8875 nm Change the number of
nodes or mdrun option -rcon or -dds or your LINCS settings.

I tried all suggestios in above error and Error page ogf Gromacs web site:

1) I changed -rcon and -dds and LINCS settings, but I have same fatal
error, again.

What is the optimum or the best values for -rcon and -dds and LINCS
settings in this case (error)?

2) I used -nt 1, this time, I had not error, but I encountered:
step 0Segmentation fault.
-----------------------------------------------------------------------------------------------
My mdp file is as follows:

title               =  CNT_H
constraints         =  all-bonds
constraint_algorithm = LINCS
integrator          =  md
dt                  =   0.001    ; ps
nsteps              =  30000  ; total : 30 ps .
nstcomm             =  1
nstxout             =  500
nstxtcout           =  500
nstvout             =  500
nstfout             =  0
nstlog              =  500
nstenergy           =  500
nstlist             =  10
ns_type             =  grid
rlist               =  0.4
rcoulomb            =  0.4
rvdw                =  0.4
Tcoupl              =  V-rescale
tc-grps                =  (NU   HHM
tau_t               =  0.2   0.2
ref_t               =  77    77
energygrps            = (NU    HHM
Pcoupl              =  no
compressibility     =  4.5e-5
gen_vel             =  yes
gen_temp            =  100.0
gen_seed            =  173529
pbc                       = xyz
coulombtype         = PME
vdwtype              = Cut-off
fourierspacing = 0.12
ewald_rtol = 1e-5
freezegrps           = (NU     HHM
freezedim            = Y Y Y   N N N
-----------------------------------------------------------------------------

How to solve this issue?

Any help will highly appreciated.