[gmx-users] mdrun

[michael zhenin]

Dear all,
I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8
processors, but it crashes after a while and refuses to reach to the end.
The error note that pops out is:

1 particles communicated to PME node 4 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


My system contains protein, ATP and Mg. I have equilibirated it for 300 ps
that were divided into 3 parts.
The first 2 parts were the NVT equilibiration (the first one was made in
order to equilibrate only the water) - 100 ps each.


The third was the NPT - 100 ps.
The system wasn't constraint.

My mdp file is :

title = OPLS wt nbd1 MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 20000000 ; 1 * 20000000 = 20000 ps, 20 ns


dt = 0.001 ; 1 fs
; Output control
nstxout = 20000 ; save coordinates every 2 ps
nstvout = 20000 ; save velocities every 2 ps
nstxtcout = 20000 ; xtc compressed trajectory output every 2 ps
nstenergy = 20000 ; save energies every 2 ps


nstlog = 20000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)


rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
ewald_rtol = 1e-05


fourierspacing = 0.12 ; grid spacing for FFT
pme_order = 6 ;
; 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 = 1.0 ; 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
morse = yes


I've searched the net for this error and didn't find any answer. Did anybody
see this error? and what should i do with it..

Thanks,

Michael
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