[gmx-users] Warning with ewald-geometry = 3dc

[anu chandra]

Dear Gromcas Users,

I am trying to run membrane protein simulation with slab geometry and EW3DC
method (ewald-geometry = 3dc). As mentioned in the article
http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0
, I have set up my system with extended Z-dimension and used pbc = xyz.
While running grompp, I experienced a warning as shown below,

WARNING 1 [file NPT.mdp]:
  With PME and ewald_geometry = 3dc you should use pbc = xy


Is it safe to neglect this warning?, Though, I carried out equilibration
with EW3DC method and pbc=xyz, the membrane got distorted. Can anybody help
me to figure what is going wrong with my simulation? Below is the mdp file
I used for equilibration.

define                  = -DPOSRES_ON
integrator              = md
dt                      = 0.001
nsteps                  = 25000
nstlog                  = 1000
nstxout                 = 1000
nstvout                 = 1000
nstfout                 = 1000
nstcalcenergy           = 100
nstenergy               = 1000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
ewald-geometry          = 3dc              ;slab geometry
pbc                     = xyz
;
tcoupl                  = V-rescale
tc_grps                 = Protein POPC Cal_CL_SOL
tau_t                   = 0.5    0.5     0.5
ref_t                   = 305.0    305.0    305.0
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0     5.0
compressibility         = 4.5e-5  0   ;0 for z-direction due to vaccum slab
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_POPC Cal_CL_SOL
;
refcoord_scaling        = com


Many thanks in advance

Anu