[gmx-users] wall_atomtype

[Manuel Valera]

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
give
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
simulations

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
wall_density?

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?

pbc=xy
nwall=2
wall_type=9-3
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






       
____________________________________________________________________________________
Now that's room service!  Choose from over 150,000 hotels
in 45,000 destinations on Yahoo! Travel to find your fit.
http://farechase.yahoo.com/promo-generic-14795097