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Hi,<br><br>Nearly all the information is in the mdp options page, but it is a bit concise.<br>The only really missing information is that there is not cut-off for the wall.<br>All atoms feel the force of one or both walls.<br><br>The density is required to determine the interaction strength of the wall<br>for the 9-3 and 10-4 options. The LJ potential is integrated over the volume<br>behind the wall or the plain of the wall, which requires a LJ particle density.<br><br>Berk<br><br><hr id="stopSpelling">Date: Mon, 21 Sep 2009 10:02:29 +0200<br>From: qiaobf@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] question about the implicit walls<br><br>
<title></title>
<div class="ecxmsgHead">Hi, <br>
<br>
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. <br>
<br>
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?<br>
<br>
regards,<br>
Baofu Qiao<br>
<br>
<span class="ecxsubject">[gmx-users] Implicit walls.</span>
<span class="ecxsender">Yves Dubief</span><br>
<span class="ecxdate">Thu, 11 Jun 2009 03:32:11 -0700<br>
</span><BR>
<span class="ecxdate">Hi,<br>
</span><BR>
</div>
<tt>I am using the implicit wall method available in 4.0.x and I cannot
</tt><tt>seem to find any published work on the method, aside from the
manual. </tt><tt>I think I have an overall understanding of the
method, but I am not </tt><tt>confident about some key details:
</tt><tt>- Is the force generated from the wall derived from a
continuum </tt><tt>representation of the wall based on the surface
density, or from a </tt><tt>lattice of virtual atoms? I am leaning
toward #1 just because it </tt><tt>works great under NPT
</tt><tt>- What is the depth of the virtual wall when wall_r_linpot=0?
Is it LJ </tt><tt>cutoff? or "zero"?
</tt><tt>- Are any of developer willing to validate the paragraph we
plan on </tt><tt>writing in my student thesis and future publications
(when it's all </tt><tt>ready)?
</tt>
<pre style=""> Thank you in advance.<br> Yves<br></pre> <br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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