[gmx-users] question about walls for a simple water box

ramon reigada at ub.edu
Tue Oct 28 13:48:43 CET 2014

Dear Gromacs users,

Unfortunately I am failing with the use of the wall options using martini force field simulations.
However, I still want to make the last attempt to work with walls. The example is simple, I built a water box with 1000 water molecules, I minimized possible contacts (steep) and then I run a constant isotropic pressure (1bar) equilibration. I checked that he water density is the correct one (about 1000 gr/l) and then I tred to simulate the water box with pbc = xy, No pressure and walls in z=0 and z=zbox.
I set the wall_atomtypes to an alkane carbon bead (C1 in the martini force field) and try 9-3, 10-4 and 12-6 potentials with different values of wall_rlin (1, 10, 10…).
I use ewald summations for the electrostatic interactions and I set ewald_geometry =3dc and wall_ewald_zfac=3. See the mdp below.
In all the attemps, the water box broke in two pieces and water escapes to large positive or negative z values outside the initial water box.

could anyone tell me what is the problme with this simple simulation?



integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.0200
nsteps                   = 200000
; number of steps for center of mass motion removal =
nstcomm                  = 1

; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 2000
nstvout                  = 2000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 2000
nstenergy                = 2000
; Output frequency and precision for xtc file =
nstxtcout                = 2000
xtc_precision            = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 =
; Selection of energy groups =
energygrps               = W

; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xy
nwall = 2
wall_atomtype = C1 C1
wall_type = 9-3
wall_density = 110 110
wall_r_linpot = 1 1
wall_ewald_zfac = 3
; nblist cut-off         =
rlist                    = 1.4
domain-decomposition     = no

; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 15
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 10
fourier_ny               = 10
fourier_nz               = 10
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no
ewald_geometry = 3dc

; Temperature coupling   =
tcoupl                   = Berendsen
; Groups to couple separately =
tc-grps                  = W
; Time constant (ps) and reference temperature (K) =
tau_t                    = 1.0
ref_t                    = 310
; Pressure coupling      =
Pcoupl                   = No

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