[gmx-users] system is not well equilibrated -Reg

[venkatesh s]

Respected Gromacs Peoples,
                     i got following error in the step mdrun nvt

               1 particles communicated to PME node 1 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.

i searched gmx user regarding the error but i cant get solution
i understand Blowing up concept (
http://www.gromacs.org/Documentation/Terminology/Blowing_Up) before nvt npt
itself error arise  what i want do ? rectifying the problem

(i followed protein&ligand tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/)


SYSTEM INFORMATIONS

ff :GROMOS96 43a1 force field
ligand -->prodrg ,antechamber (charge)
FOUR PROTEIN (USING :CHAINSEP -TER ) ONE LIGAND

TOTAL NUMBER OF ATOM & RESIDUE
chain  #res #atoms

  1 'A'   661   5352
  2 'B'   686   5550
  3 'Z'     4      4
  4 'C'   148   1236
  5 'D'   225   1706
  6 'E'   236   1817
  7 ligand        45

WATER MODEL :SPC
BOX TYPE  : DODECAHEDRON


em out put
*********************************************************************************************
Steepest Descents converged to Fmax < 1000 in 8222 steps
Potential Energy  = -7.0989005e+06
Maximum force     =  9.8313232e+02 on atom 14319
Norm of force     =  1.3521968e+01

em_cg out put
*********************************************************************************************
Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 27 steps
Potential Energy  = -7.1276280e+06
Maximum force     =  7.3455371e+02 on atom 14317
Norm of force     =  1.3223733e+01

EM .MDP
**********************************************************************************************
; LINES STARTING WITH ';' ARE COMMENTS
title        = Minimization    ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force <
10.0 kJ/mol
emstep      = 0.01      ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to
perform
energygrps    = system    ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 1            ; Frequency to update the neighbor list and
long range forces
ns_type        = grid        ; Method to determine neighbor list (simple,
grid)
rlist        = 1.0        ; Cut-off for making neighbor list (short range
forces)
coulombtype    = PME        ; Treatment of long range electrostatic
interactions
rcoulomb    = 1.0        ; long range electrostatic cut-off
rvdw        = 1.0        ; long range Van der Waals cut-off
pbc         = xyz         ; Periodic Boundary Conditions (yes/no)
************************************************************************************************
EM_CG.MDP
************************************************************************************************
; LINES STARTING WITH ';' ARE COMMENTS
title        = Minimization    ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator    = cg        ; Algorithm
emtol        = 1000.0      ; Stop minimization when the maximum force <
10.0 kJ/mol
emstep          = 0.01      ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to
perform
energygrps    = Protein UNK    ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist        = 1            ; Frequency to update the neighbor list and
long range forces
ns_type        = grid        ; Method to determine neighbor list (simple,
grid)
rlist        = 1.0        ; Cut-off for making neighbor list (short range
forces)
coulombtype    = PME        ; Treatment of long range electrostatic
interactions
rcoulomb    = 1.0        ; long range electrostatic cut-off
rvdw        = 1.0        ; long range Van der Waals cut-off
pbc            = xyz         ; Periodic Boundary Conditions (yes/no)
**************************************************************************************************

NVT.MDP
***************************************************************************************************
; 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
energygrps  = Protein UNK
; Bond parameters
continuation    = no            ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; 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 cells
nstlist     = 5         ; 10 fs
rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.4       ; 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
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
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    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed
********************************************************************************************


-- 
Regards,*
*S.VENKATESH,