[gmx-users] Hole in the membrane during initial equilibration

[anu chandra]

Dear Gromacs users,

I am trying to run a membrane protein simulation with  slab geometry along
Z-axis, due to ion asymmetry. The simulation box was well equilibrated
before implementing the slab geometry. The box dimension before the
addition of slab was -  ' 112.347  112.347  126.531  90.00  90.00  90.00'
and I added a 2 nm vacuum slab along Z-axis by using 'editconf' command -
editconf -f input.pdb -o ouput.pdb -c -box 11.2347  11.2347  14.6531.
Later, I tried to carry out NVT equilibration after 1000 steps initial
minimization. Unfortunately, a number holes formed in the membrane which
eventually leads the mixing up of water from top and bottom layer. Below, I
copied the NVT mdp file used for equilibration. Please help me to figure
out error with my simulation.

###############################################################

define                  = -DREST_ON -DNVT  ; restrain the protein here
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
verlet-buffer-tolerance = -1
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
ewald-geometry          = 3dc
pbc                     = xy
;
nwall                    = 1
wall-type                = 10-4
wall-r-linpot            = -1
wall-atomtype            = CT3
wall-density             = 5
wall-ewald-zfac          = 3
;
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
;
constraints             = h-bonds
constraint_algorithm    = LINCS
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_POPC Cal_CL_SOL
;
gen-vel                 = yes
gen-temp                = 305.0
gen-seed                = -1
;
refcoord_scaling        = com

##############################################################



Many thanks in advance

Anu