[gmx-users] wall_atomtype

Berk Hess gmx3 at hotmail.com
Thu Apr 12 10:16:39 CEST 2007

>From: Manuel Valera <valeraml at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] wall_atomtype
>Date: Wed, 11 Apr 2007 18:53:15 -0700 (PDT)
>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

The mdp options page of CVS:
describes the wall mdp parameters.

wall_atomtype can be an existing atom type of the force field,
or you can add a new atom type.


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