GROMACS version:2018.3
GROMACS modification: Yes/No
Hello all,
I’m running periodic graphene (box: 5.15755 * 5.10480 * 5.20000 nm) in NVT assemble.
Problems with Domain Decomposition.
The bond interaction distance appears to be incorrect, which results in an error in the calculation of the minimum cell size.
Initializing Domain Decomposition on 32 ranks
Dynamic load balancing: locked
Minimum cell size due to atom displacement: 0.433 nm
Initial maximum inter charge-group distances:
two-body bonded interactions: 7.084 nm, Exclusion, atoms 927 1007
multi-body bonded interactions: 7.084 nm, Angle, atoms 927 1007
Minimum cell size due to bonded interactions: 7.793 nm
Guess for relative PME load: 0.23
Will use 24 particle-particle and 8 PME only ranks
This is a guess, check the performance at the end of the log file
Using 8 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 24 cells with a minimum initial size of 9.741 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0
The error seems to originate from a two-body bonded interaction (7.084 nm) between atoms 927 and 1007.But in .top file there are no bond between atom 927 and 1007 (and should not have bond according to structure of graphene) .
position of atom 927 and 1007 are in figure
Considering 7.084nm ≈ 5nm * sqrt(2), I wonder the incorrect distance of the atomic interaction is caculated as the distance between the two atoms inside the box(7.084 nm) but not the distance cross the periodic boundary(~0.2nm)
Periodic boundary conditions is set in mpd file, but it dosen’t work.
How could I fix it?
Other files:
sbatch.sh files:
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
srun hostname -s | sort -n > slurm.hosts
gmx_mpi grompp -f NVT.mdp -c em.gro -p GRA.top -o npt.tpr
mpirun -n 32 -machinefile slurm.hosts gmx_mpi mdrun -v -s npt.tpr -o npt.trr -c npt.gro
mdp file:
title = OPLS NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 40000000 ; 1 fs * 40000000 = 40 ns
dt = 0.001 ; 1 fs
; Output control
nstxout = 2000 ; save coordinates every 20 ps
nstvout = 2000 ; save velocities everys 20 ps
nstenergy = 2000 ; save energies every 20 ps
nstlog = 2000 ; update log file every 20 ps
; Bond parameters
continuation = yes ; first dynamics run
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
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; 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 = Berendsen ; modified Berendsen thermostat
tc-grps = K SOL CL GRA ; two coupling groups - more accurate
tau_t = 0.1 0.1 0.1 0.1 ; time constant, in ps
ref_t = 300 300 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
freezegrps =GRA
freezedim =Y Y Y