[gmx-users] 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

[Farideh Badalkhani Khamseh]

Dear GROMACS users.

I am trying to perform MD simulations on a PEGylated dendrimer. At first, I performed energy minimization with

emtol = 1000 kJ/mol/nm.

I did not gent any error in EM, NVT (1 ns), and NPT (1 ns) equilibrations. But the simulation crashed  relatively early (within 1 ns). Therefore, I performed successive Steep and CG minimizations until the system was minimized at emtol = 80 kJ/mol/nm. Again, I did not get any error during NVT and NPT equilibrations. This time production MD crashed after 10 ns and I got the following error:

DD  step 5489999 load imb.: force  0.2%
           Step           Time
        5490000    10980.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
    2.27616e+03    7.97871e+03    6.08238e+03    3.55375e+01    2.21395e+03
     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
    3.79715e+04    3.35801e+05   -1.16286e+04   -2.68521e+06    8.57466e+03
      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature
   -2.29590e+06    4.43034e+05   -1.85287e+06   -1.63147e+06    3.10476e+02
 Pres. DC (bar) Pressure (bar)   Constr. rmsd
   -1.10990e+02    9.76046e+01    3.84574e-06

Constraint error in algorithm Lincs at step 5491696
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 5491698
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 5491700
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 5491701
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 5491702
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 5491703
Wrote pdb files with previous and current coordinates
Constraint error in algorithm Lincs at step 5491704
Wrote pdb files with previous and current coordinates

-------------------------------------------------------
Program:     gmx mdrun, version 2019.3
Source file: src/gromacs/ewald/pme-redistribute.cpp (line 282)
MPI rank:    0 (out of 2)

Fatal error:
1 particles communicated to PME rank 0 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.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


The md.mdp file is as follows:

title                   = G3ACE-16PEG MD
; Run parameters
integrator              = md        ; leap-frog integrator
nsteps                  = 50000000     ; 2 * 50000000 = 100 ns
dt                      = 0.002     ; 2 fs
; Output control
nstxout                 = 5000        ; save coordinates every 10 ps
nstvout                 = 5000        ; save velocities every 10 ps
nstfout                 = 5000      ; nstvout, and nstfout
nstenergy               = 5000      ; save energies every 10.0 ps
nstlog                  = 5000      ; update log file every 10.0 ps
nstxout-compressed      = 5000      ; save compressed coordinates every 10.0 ps
compressed-x-grps       = System    ; save the whole system
; Bond parameters
continuation            = yes       ; Restarting after NPT
constraint_algorithm    = lincs     ; holonomic constraints
constraints             = h-bonds   ; bonds involving H are constrained
lincs_iter              = 1         ; accuracy of LINCS
lincs_order             = 4         ; also related to accuracy
; Neighborsearching
cutoff-scheme           = Verlet    ; Buffered neighbor searching
ns_type                 = grid      ; search neighboring grid cells
nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb                = 1.2       ; short-range electrostatic cutoff (in nm)
rvdw                    = 1.2       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype             = PME       ; 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                 = Dendrimer Water_and_ions    ; two coupling groups - more accurate
tau_t                   = 0.1     0.1                 ; time constant, in ps
ref_t                   = 310     310                 ; 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                = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel                 = no        ; Velocity generation is off
----------------------------------------------------------------------------------------------------------------------


Any help will be greatly appreciated.


Kind regards,

Farideh Khamseh