[gmx-users] question about the implicit walls

Berk Hess gmx3 at hotmail.com
Mon Sep 21 10:53:27 CEST 2009


Nearly all the information is in the mdp options page, but it is a bit concise.
The only really missing information is that there is not cut-off for the wall.
All atoms feel the force of one or both walls.

The density is required to determine the interaction strength of the wall
for the 9-3 and 10-4 options. The LJ potential is integrated over the volume
behind the wall or the plain of the wall, which requires a LJ particle density.


Date: Mon, 21 Sep 2009 10:02:29 +0200
From: qiaobf at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] question about the implicit walls



Is anyone who can clear the "Walls" feature in the gmx 4.0.x? Same as
Yves (see the end), I cannot find any related reference or publication
citing it. 

Generally the potential on wall is in continuum format. But if it is
also true here,  what the "wall_density" for?  I guess it is based on a
lattice model. If I want to build silicon or graphene walls, what kind
of values is suitable for them? Any reference?


Baofu Qiao

[gmx-users] Implicit walls.
Yves Dubief

Thu, 11 Jun 2009 03:32:11 -0700


I am using the implicit wall method available in 4.0.x and I cannot
seem to find any published work on the method, aside from the
manual. I think I have an overall understanding of the
method, but I am not confident about some key details:
- Is the force generated from the wall derived from a
continuum representation of the wall based on the surface
density, or from a lattice of virtual atoms? I am leaning
toward #1 just because it works great under NPT
- What is the depth of the virtual wall when wall_r_linpot=0?
Is it LJ cutoff? or "zero"?
- Are any of developer willing to validate the paragraph we
plan on writing in my student thesis and future publications
(when it's all ready)?

   Thank you in advance.
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