[gmx-users] problem with tutorial KALP-15 in DPPC

[serena]

Hi all
I'm doing the GROMACS tutorial KALP-15 in DPPC. I've done the steps until
the energy minimization, so now I've my system at an energy minimum and  I'm
doing the equilibration with this nvt.mdp:

define		= -DPOSRES  ; position restrain the protein and lipid
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 50000		; 2 * 50000 = 100 ps
dt		= 0.002		; 2 fs
; Output control
nstxout		= 100		; save coordinates every 0.2 ps
nstvout		= 100		; save velocities every 0.2 ps
nstenergy	        = 100		; save energies every 0.2 ps
nstlog		= 100		; update log file every 0.2 ps
; Bond parameters
continuation	 = no		        ; first dynamics run
 constraint_algorithm = lincs	; holonomic constraints 
 constraints	= h-bonds	        ; vecchio all bonds (even heavy atom-H bonds)
constrained
 lincs_iter	= 1		            ; accuracy of LINCS
 lincs_order	= 4		            ; also related to accuracy
; Neighborsearching
ns_type		= grid		; search neighboring grid cels
nstlist		= 5		    ; 10 fs
rlist		= 1.2		; vecchio: 1.0 short-range neighborlist cutoff (in nm)
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 electrostat
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 DPPC SOL_CL	; three coupling groups - more accurate
tau_t		= 0.1	0.1	0.1	        ; time constant, in ps
ref_t		= 323 	323	323	        ; 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
; Dispersion correction
 DispCorr	= EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel		= yes		; assign velocities from Maxwell distribution
gen_temp	= 323		; temperature for Maxwell distribution
gen_seed	= -1		; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm		= 1
comm-mode	= Linear
comm-grps	= Protein_DPPC SOL_CL

I've done this command:
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
mdrun -deffnm nvt

but I received this error:
starting mdrun 'Protein in water'
50000 steps,    100.0 ps.

step 0: Water molecule starting at atom 101831 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 0: Water molecule starting at atom 99524 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Fatal error:
1 particles communicated to PME node 8 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.

What means of this error? How to fix it?
thank you


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