[gmx-users] nwall=2 calculation

[Stephen Chan]

Hi all,

I'm trying to run simulation on a bilayer system. I managed to 
incorporate all atoms inside the simulation box and passed the 
minimization step. However, by the end of the equilibrium steps, the 
third box vector (z-direction) was nearly 3 times than the original one. 
I'm using ewald-geometry 3DC and the lipid bilayer is parallel to the 
x-y plane. The manual seems suggesting that a box height of 3 times the 
slab height is ok. However, the calculation speed becomes terribly slow, 
when compared to the calc without the walls. Here is the mdp of the last 
equilibrium step:

integrator              = md
dt                      = 0.002
nsteps                  = 2000000
nstlog                  = 1000
nstxout                 = 0
nstvout                 = 0
nstfout                 = 0
nstcalcenergy           = 100
nstenergy               = 1000
nstxout-compressed      = 10000
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.0
coulombtype             = pme
rcoulomb                = 1.0
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 0.9
rvdw                    = 1.0
;
tcoupl                  = berendsen
tc_grps                 = PROT   MEMB   SOL_ION
tau_t                   = 1.0    1.0    1.0
ref_t                   = 310   310   310
;
pcoupl                  = berendsen
pcoupltype              = semiisotropic
tau_p                   = 5.0
compressibility         = 0.0     4.5e-5
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = PROT   MEMB   SOL_ION
;
refcoord_scaling        = com
;
pbc                     = xy
nwall                   = 2
wall-type               = 10-4
wall-density            = 5  5
wall-atomtype           = OT OT
ewald-geometry          = 3dc

I wonder if I have used wrong parameters somewhere.

Regards,

Stephen