[gmx-users] Reg:walls and pbc xy

vinothkumar mohanakrishnan kmvinoth at gmail.com
Tue Nov 2 07:19:48 CET 2010

Hi Gromacians

I want to create a liquid-liquid interface and study its properties. Hence i
combined two boxes ( say water and DCE). The two boxes  are well
equilibrated before merging and i created an interface. Now i want to
perform energy minimisation for the interface by appling pbc in the xy
direction and using walls. ( If i apply pbc in all the directions i get two
interfaces where as i need only one interface hence i am applying it only on
the xy direction and removing the boundary condition in the Z
direction.).When i performed the energy minimisation for the interfacial
system but i found that my system is exploding (several PDB files are
written while running mdrun is executed) and i dont know why?.There is no
issue when i use pbc in all directions. below is my em.mdp file. any help is
highly appreciated.

integrator    = steep
emtol        = 40.0
emstep          = 0.01
nsteps        = 10000
nstxout        = 100
nstvout        = 100
nstfout        = 100
nstlog        = 100
nstenergy    = 100
nstlist        = 5
ns_type        = grid
rlist        = 1.0
coulombtype    = PME
rcoulomb    = 1.0
vdwtype        = Cut-off
rvdw        = 1.0
ewald_geometry    = 3dc
nwall        = 2
wall_type    = 9-3
wall_r_linpot    = 1
wall_atomtype   = opls_966 opls_968
wall_density    = 9-3 9-3
wall_ewald_zfac    = 3
pbc        = xy
fourierspacing  = 0.18

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