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Hi,<br><br>For all interactions except for the PME mesh part there is no pbc in z.<br>For PME mesh there is periodicity in z.<br><br>For c) there are several options.<br>One issue is that the DD setup is not very smart (yet)<br>and it might decompose is z. If this is case, use the -dd option<br>of mdrun to preferable decompose in x and possibly also in y.<br><br>Another option would be to use a slightly longer cut-off and a coarser grid.<br>Or simply do not use separate PME nodes.<br><br>Berk<br><br><hr id="stopSpelling">Date: Mon, 21 Sep 2009 15:09:13 +0200<br>From: qiaobf@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: Re: [gmx-users] question about the implicit walls<br><br>
HI Berk,<br>
<br>
Thanks for your reply!<br>
<br>
Questions related the implicit Walls. <br>
a) When I use PBC =xyz in combination with nwall=2, I get the following
error<br>
ERROR: walls only work with pbc=xy<br>
But If I use pbc=xy, there is no periodic image in the Z
direction, why should we use "wall_ewald_zfac"=2~3? <br>
c) Even though I have used half of the processors for -npme, there is
still more than 20% is lost due to PME have more work to do. Is there
any idea to improve the performance?<br>
<br>
The following is the parameters for the walls I try to simulate the
graphine substrate.<br>
<br>
; WALLS<br>
; Number of walls, type, atom types, densities and box-z scale factor
for Ewald<br>
nwall = 2<br>
wall_type = 9-3<br>
wall_r_linpot = 0<br>
wall_atomtype = opls_135 opls_135<br>
wall_density = 114 114<br>
wall_ewald_zfac = 3<br>
<br>
<br>
<br>
Berk Hess wrote:
<blockquote cite="mid:COL113-W39497AACDB8C5B049BDA4C8EDD0@phx.gbl">
<pre>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>Date: Mon, 21 Sep 2009 10:02:29 +0200<br>From: <a class="ecxmoz-txt-link-abbreviated" href="mailto:qiaobf@gmail.com">qiaobf@gmail.com</a><br>To: <a class="ecxmoz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Subject: [gmx-users] question about the implicit walls<br><br><br><br><br><br><br> <br> <br><br><br><br><br>Hi, <br><br><br><br>Is anyone who can clear the "Walls" feature in the gmx 4.0.x? Same as<br>Yves (see the end), I cannot find any related reference or publication<br>citing it. <br><br><br><br>Generally the potential on wall is in continuum format. But if it is<br>also true here, what the "wall_density" for? I guess it is based on a<br>lattice model. If I want to build silicon or graphene walls, what kind<br>of values is suitable for them? Any reference?<br><br><br><br>regards,<br><br>Baofu Qiao<br><br><br><br>[gmx-users] Implicit walls.<br>Yves Dubief<br><br>Thu, 11 Jun 2009 03:32:11 -0700<br><br><br><br>Hi,<br><br><br><br><br>I am using the implicit wall method available in 4.0.x and I cannot<br>seem to find any published work on the method, aside from the<br>manual. I think I have an overall understanding of the<br>method, but I am not confident about some key details:<br>- Is the force generated from the wall derived from a<br>continuum representation of the wall based on the surface<br>density, or from a lattice of virtual atoms? I am leaning<br>toward #1 just because it works great under NPT<br>- What is the depth of the virtual wall when wall_r_linpot=0?<br>Is it LJ cutoff? or "zero"?<br>- Are any of developer willing to validate the paragraph we<br>plan on writing in my student thesis and future publications<br>(when it's all ready)?<br><br> Thank you in advance.<br> Yves<br> <br>_________________________________________________________________<br>Express yourself instantly with MSN Messenger! Download today it's FREE!<br><a class="ecxmoz-txt-link-freetext" href="http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/">http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/</a><br> </pre>
<pre><hr width="90%" size="4"><br>_______________________________________________<br>gmx-users mailing list <a class="ecxmoz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a class="ecxmoz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a class="ecxmoz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a class="ecxmoz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a class="ecxmoz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></pre>
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