[gmx-users] Help: Anyone worked with "Wall"?

Huaichen(Bobby) Zhang bobbyhczhang at gmail.com
Thu Apr 5 22:08:02 CEST 2012

Dear all,

I'm trying to simulate with pbc=xy and I need two walls. My settings are as

pbc                 =  xy
nwall               =  2
wall_atomtype       =  C C
wall_type           =  9-3
wall_r_linpot       =  -1 -1
wall_density        =  20 20
wall_ewald_zfac     =  3

The problem is how to define wall_atomtype in my topology file (top/itp)? A
want to have this solid carbon wall with 9-3 potential. Where in my top/itp
file can I define such atoms? This is my top file:

#include "ffG53a6.itp"
#include "spc.itp"

[ system ]
Pure Water with walls

[ molecules ]
SOL    216

When I gmxdump the generated tpr file, I saw no C atoms are defined; and it

   wall_atomtype[0]     = 2
   wall_atomtype[1]     = 2

which corresponds to the hydrogen atom in my top file. And according to my
forcefield, the LJ parameters for H is 0,0. So there is basically no wall.
When I tried to simulate with this setting, the water molecules went out of
the box (in z direction) and moved far away. And according to g_energy,
there is no interaction energy between water and wall. So there indeed is
no wall.

Can you help me with defining wall atom? If you have already finished any
tasks with this wall algorithm, can you kindly attach your topology files
to me?

Soooooooooooooooooo many thanks!!!!!!!!!!!!!!!!!

Huaichen(Bobby) ZHANG

+31 648478172
MSc Sustainable Energy Engineering
Royal Institute of Technology (Sweden)
Eindhoven University of Technology (Netherland)
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