[gmx-users] wall_atomtype

Manuel Valera valeraml at yahoo.com
Thu Apr 12 03:53:15 CEST 2007

Greetings to All

I have a question about a new feature in the cvs code
and I was wondering if there was anybody who could
me a hand of a bit of help.
Thanks in advanced.

I am working on a project that involves simulation of
confined water between two hydrophobic surfaces.
I noticed that recently there was an addition to the
gromacs source code that would allow for this kind of

I downloaded the cvs source code to try out this new
feature, ran a small simulation of water with pbc=xy
and no surfaces and could see the water evaporate as
was expected

The problems occurs when I need to add surfaces to the

simulation. There are some new variables that I don't
know how to set and I have not been able to figure
this out from the source code.

What are the appropriate values for wall_atomtype?
I want to have a LJ interaction between the wall and
the oxygen atom in
the water molecule.
How can I do this with this new feature?

In the function do_walls we have (file wall.c)

    if (ir->wall_type == ewt93) {
      fac_d[w] = ir->wall_density[w]*M_PI/6;
      fac_r[w] = ir->wall_density[w]*M_PI/45;
    } else if (ir->wall_type == ewt104) {
      fac_d[w] = ir->wall_density[w]*M_PI/2;
      fac_r[w] = ir->wall_density[w]*M_PI/5;
Where are these factor coming from, is there a
reference that I can look at?

What would be appropriate values for the variable

Would these be the appropriate changes to my
grompp.mpd file to get
this feature working of is there anything else that I
need to add?

wall_atomtype = ? ?
wall_density = ? ?

I apologized if these are too many questions!!

I realized this a very new feature and probably it is
not well tested, yet I would like to try it out and
see if I can use this for my project

Any help would be really appreciated.

Thanks a lot.
Kind regards,

Manuel Valera

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