GROMACS version: 2020.3

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Hi all,

I have been getting an error saying “165 particles communicated to PME rank 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x”, when submitting a job using more than one gpu core, using -ntmpi 2 or -ntmpi 4. That said, the simulation works fine with -ntmpi 1. The GPU is a Tesla K80. I am running the job with: gmx mdrun -deffnm md -ntmpi 2 -ntomp 5 -v

My system comprises a protein complex in a cubic box of water and sodium chloride, using DES-amber force field. I am using the mdp file below:

title = job

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 50000000 ; (100 ns)

dt = 0.002 ; 2 fs

; Output control

nstxout = 0 ; suppress bulky .trr file by specifying

nstvout = 0 ; 0 for output frequency of nstxout,

nstfout = 0 ; 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 = Protein Water_and_Ions ; two coupling groups - more accurate

tau_t = 0.1 0.1 ; time constant, in ps

ref_t = 300 300 ; 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 = EnerPres ; account for cut-off vdW scheme

; Velocity generation

gen_vel = no ; Velocity generation is off

Please let me know if you need any more information to help troubleshoot this problem.

Thanks

Arash