From: Manuel Valera <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
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
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
The mdp options page of CVS:
share/html/online/mdp_opt.html
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.
Berk.
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