Hi, Berk<br><br>Thank you for your reply, finally I solved this by modifying the mdp options.<br><br>'Cause I want to use PME in 2-dimensional periodic system to compute electrostatic, I have to <br>set up the virtual walls with mdp option nwalls=2 in Gromacs. It succeeded to set up the simualtion system.<br>
<br>Originally, I constructed the walls of monocrystal SI with diamond lattice structure, but setting nwalls=0 and pbc=xy, so it happened that the z-direction component of box size in the resulting gro file is 0.00000.<br>
<br>But, could I set nwalls=2, but with wall_density=0.0 to just with two virtual walls without any<br>density, i.e. without wall atoms?? So that the additonal virtual walls the mdrun added will not affect my system 'cause I already have two walls.<br>
---------------------------------------------------------<br>nwalls =2<br>wall_type = 10-4 ;<br>wall_atomtype = SI SI ;<br>wall_density = 7.12 7.12 ; nm^{-2}, number density, 200 atom in 5.3x5.3nm^2<br>
---------------------------------------------<br><br clear="all">Regards,<br>Yinhe Zhang<br>
<br><br><div class="gmail_quote">On Wed, May 6, 2009 at 4:54 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
Hi,<br><br>I tried to reproduce this, but I did not succeed.<br>mdrun always seems to write the correct z size in all output files.<br><br>Are you sure mdrun outputs a file (and which file, if so),<br>or is it another Gromacs program that produced the file with 0 z size?<br>
<br>You can simply manually correct the size in the file.<br>But please report back which program produced which incorrect file.<br><br>Berk<br><br><hr>Date: Wed, 6 May 2009 00:39:18 +0800<br>From: <a href="mailto:crickzhang1@gmail.com" target="_blank">crickzhang1@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>Subject: [gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after<div><div></div><div class="h5">
<br><br><div>Hi, all</div>
<div> </div>
<div>There are some things confusing and resulting in error when I run mdrun for energy minization and md.</div>
<div> </div>
<div>I use Gromacs 4.0.4 to simulate electroosmotic flow in slab geometry with only 2 dimensional </div>
<div>periodic boundary (x and y), the system is aqueous solution with some ions, eg. CL- and Na+,</div>
<div>flowing through a plate channel, with external electrical field applied along x-direction, the height of channel</div>
<div>is z-direction. </div>
<div> </div>
<div>Coulomb interactions are computed with PME, and use pbc=xy, after running EM, all ouput tpr box sizes </div>
<div>in z-direction becomes zero, eg. originally the box size is 4.50000,4.50000,3.90000, after EM, it became</div>
<div>4.50000,4.50000,0.00000. so I can't use the output gro of EM for the MD run.</div>
<div> </div>
<div>Did someone encounter this before and can give me some suggestion for my mdp setup?</div>
<div> </div>
<div>Thanks in advance.</div>
<div> </div>
<div>(sorry for bad English expressions)</div>
<div> </div>
<div>some options for mdp file of mine are here:</div>
<div> </div>
<div>pbc = xy</div>
<div>rlist = 1.1 </div>
<div>rcoulomb = 1.1 <br>rvdw = 1.1 </div>
<div> </div>
<div>; electrostatics<br>coulombtype = PME </div>
<div>fourierspacing = 0.12 </div>
<div>;fourier_nx = </div>
<div>;fourier_ny = <br>fourier_nz = 30<br>pme_order = 4 <br> dim</div>
<div>ewald_geometry = 3dc ; IMPORTANT</div>
<div>optimize_fft = yes ; </div>
<div> </div>
<div>nwall = 2 <br>wall_type = 10-4 <br>;wall_r_linpot = <br>wall_atomtype = SI SI <br>wall_density = 7.12 7.12 <br>
wall_ewald_zfac = 3 </div>
<div> </div>
<div>; NEMD<br>acc_grps = WA WAb WAu<br>accelerate = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0<br>freezegrps = WA WAb WAu<br>freezedim = Y Y Y Y Y Y Y Y Y<br>
</div>
<div>; Electric fields <br>E_x = 1 -0.55 0</div>
<div></div>
<div> </div>
<div><br clear="all">Regards,<br>Yinhe Zhang<br></div><br></div></div><div class="hm"><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a></div>
</div>
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