[gmx-users] Walls and center of mass motion

Anders Støttrup Larsen anders.sl at gmail.com
Fri Oct 13 15:15:40 CEST 2017

Hi all

I have been trying to simulate a system containing two walls and a
slab/vacuum. During the simulation water from the slab diffuses into the
vacuum as intended. The problem is that this causes the slab to move in the
z-direction and eventually crash into one of the walls. The slab has a
thickness of 60 Å and there is approximately 220 Å of vacuum at both sides
of the slab.

When using *nwall=2 *GROMACS turns off center of mass motion removal in the
z-direction, is there any way to turn this back on? Or some other solution
that makes sure the slab doesn’t move?

I have attached the relevant part of the mdp.

comm-mode               = Linear

pbc                           = xy

ewald-geometry          = 3dc

nwall                         = 2

wall-type                    = 12-6

wall-r-linpot                = -2

wall-atomtype            = c c

wall-density               = 40 40

wall-ewald-zfac          = 3



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