Can anyone help me? I am trying to perform MD simulation. My glicoprotein is a dimer (two different chains). When I run NVT with restriction this fatal error appears:

"Fatal error:

12 particles communicated to PME rank 10 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"

mdp file looks like this:

define = -DPOSRES ;

integrator = md ;

dt = 0.002 ;

nsteps = 50000 ;

nstxout = 10000 ;

nstvout = 10000 ;

nstenergy = 500 ;

nstlog = 500 ;

energygrps = glicoprot Water_and_Ions ;

nstlist = 10

ns_type = grid

pbc = xyz

rlist = 1.0

coulombtype = PME ;

pme_order = 4 ;

fourierspacing = 0.16 ;

rcoulomb = 1.0

vdw-type = Cut-off

rvdw = 1.0

tcoupl = v-rescale ;

tc-grps = glicoprot Water_and_Ions ;

tau_t = 0.1 0.1 ;

ref_t = 300 300 ;

DispCorr = EnerPres ;

pcoupl = no ;

gen_vel = yes ;

gen_temp = 300 ;

gen_seed = -1 ;

constraints = all-bonds ;

continuation = no ;

constraint_algorithm = lincs ;

lincs_iter = 1 ;

lincs_order = 4 ;

cutoff-scheme = verlet

I have already reduced dt = 0.002 to 0.001 but it didn't solve.

Can anyone suggest another option?

regards,