[gmx-users] no domain decomposition

[soumadwip ghosh]

Hi all,
         I am simulating a DNA encapsulated in a carbon nanotube in the
presence of some fillers. Previously I was having this domain decomposition
error every time I was attempting an mdrun. There were some problems in the
initial structure which I fixed according to the suggestion of Justin and
Tsjerk and now energy minimization and position restrained dynamics are all
going well. Today, I took the npt.gro file and tried the production run
with the following mdp file..

title = dna in water
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000000              ;2 * 25000000 = 50000 ps, 50 ns
dt              = 0.001         ; 2 fs
; Output control
nstxout         = 1000          ; save coordinates every 2 ps
nstvout         = 1000          ; save velocities every 2 ps
nstxtcout       = 1000          ; xtc compressed trajectory output every 2
ps
nstenergy       = 1000          ; save energies every 2 ps
nstlog          = 1000          ; update log file every 2 ps
; Bond parameters
continuation    = yes           ; Restarting after NPT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet        ; search neighboring grid cells
vdwtype         = cutoff        ; 10 fs
vdw-modifier    = force-switch
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
rvdw            = 1.2           ; short-range electrostatic cutoff (in nm)
rvdw-switch     = 1.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME
rcoulomb        = 1.2           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = SYSTEM        ; two coupling groups - more accurate
tau_t           = 0.1           ; time constant, in ps
ref_t           = 300           ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = no            ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no            ; Velocity generation is off
energygrps      = UNK a1 t2 c3 g4 LIG

I obtained the tpr file using grompp but my mdrun crashed telling,
A charge group moved too far between two domain decomposition step
which means your system is not well equilibrated.

Then I checked the pressure and temperature of the npt.edr file and the
pressure value was

0.67 with an error bar of 0.97 while the desired pressure was 1.0 bar. Is
this the reason why mdrun is crashing? I have done NPT for 10 ns and still
the pressure has not converged. What is going wrong here ? I am using
gromacs 5.0.5 in combination with CHARMM 27 force field.

As far as I understand my system is not equilibrated properly. Should I
perform NPT for a longer time and see whether the pressure is getting
converged or the problem is something else?

Any kind of help would be appreciated.

Thanks and regards,
Soumadwip Ghosh
Research Fellow,
IITB
Mumbai
India