MARTINI: 1 particles communicated to PME rank 17 are more than 2/3 times the cut-off

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1

GROMACS version: gmx mdrun, VERSION 5.0.7 (double precision)
GROMACS modification: Yes/No

I am performing MD simulations of two proteins in water and I am using MARTINI force field for it. I am gettting this error.

Fatal error:
1 particles communicated to PME rank 17 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
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 MDP file that I am using is:

define                  = -DPOSRES_ON  ; position restrain the protein
; Run parameters
integrator              = md        ; leap-frog integrator
nsteps                  = 50000     ; 2 * 50000 = 100 ps
dt                      = 0.02     ; 2 fs
; Output control
nstxout                 = 500       ; save coordinates every 1.0 ps
nstvout                 = 500       ; save velocities every 1.0 ps
nstenergy               = 500       ; save energies every 1.0 ps
nstlog                  = 500       ; update log file every 1.0 ps
; Bond parameters
continuation            = yes       ; Restarting after NVT 
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 scheme
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                  = V-rescale             ; modified Berendsen thermostat
tc-grps                 = Protein Non-Protein   ; 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                   = 4.0                   ; time constant, in ps
ref_p                   = 1.0                   ; reference pressure, in bar
compressibility         = 4.5e-5                ; isothermal compressibility of water, bar^-1
refcoord_scaling        = com
; Periodic boundary conditions
pbc                     = xyz       ; 3-D PBC
; Velocity generation
gen_vel                 = no        ; Velocity generation is off

I have a question (maybe related to the error or maybe not): While performing MD simulations with MARTINI, it is suggested to use 20-40 fs picoseconds, but while performing equilibriation, what time step is advised ?

I am not sure where to port this question but since it is related to running the MD I am posting it here.

Please help me resolve this issue.

Thank you and wish you a very happy new year (belated).

Yours sincerely,
Ved

2

For minimisation, I would typically start with 4 or 5 fs, then equilibrate with 10 fs and then 20 fs. Large timesteps of 20 fs may be an issue in some cases but might work in others. Start with a small time step and then gradually increase.