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<div>Hi</div>
<div>As I posted the command list earlier, to create the box</div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box 6.0 6.0 6.0</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">So, I think Justin's case is not the same as mine.</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Thank you</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Lin</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Message: 1<br>
Date: Fri, 01 Jan 2010 18:53:53 -0500<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] Simulation Box break into 16 domains =><br> Gromacs 3.3.3<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4B3E8B11.7040700@vt.edu">4B3E8B11.7040700@vt.edu</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA"></span> </div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">Mark Abraham wrote:<br>
> Chih-Ying Lin wrote:<br>>><br>>><br>>><br>>><br>>> Hi<br>>> Sorry that i have posted the same message for several times.<br>>><br>>> I used Gromacs version 3.3.3.<br>>> My simulation system = one protein + 20 ligand + water molecules ( 7x<br>
>> 7x 7<br>>> )<br>>> MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total<br>>> After doing the energy minimization, => the potential energy is extremely<br>>> high ( say, ten to the 9th order )<br>
>> I visualized the " Simulation-System-EM-solvated.gro " after the energy<br>>> minimization.<br>>> Then, I found that the Simulation Sysmtem is devided into 16 domains very<br>>> clearly and the molecules (protein, ligand, and water) break into<br>
>> atoms in<br>>> the boundaries.<br>>> I have checked that the 20 ligands are not overlapped each other and<br>>> are not<br>>> overlapped with protein from the beginning.<br>><br>> Chih-Ying sent me before and after .gro files off-list, and the<br>
> structure really has done something like this (pic attached). After EM,<br>> the cubic simulation cell has partitioned four times along each side,<br>> and within each small cube, the waters have contracted as if to minimize<br>
> surface area. The result is as if each small cube did an EM in isolation<br>> of any other such cube.<br>><br>> Are you sure you are using a 3.3.3 mdrun? Consult the top part of the<br>> log file. I'd guess the most likely problem is that you're seeing some<br>
> bizarre artefact of your MPI or installation. How was GROMACS<br>> configured? Did you use shared libraries? Try a version without. Try<br>> single-processor grompp+mdrun.<br>><br>> If there's no light shed by the above, please send me your input protein<br>
> and ligand structure files, and your pre-EM .tpr and I'll see if I can<br>> reproduce your workflow or result.<br>><br>> Mark<br>><br>></span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">I have a strong suspicion that this all derives from the incorrect editconf<br>
command posted earlier. I saw something like this once, long ago, before I knew<br>what I was doing :) The problem I had stemmed from incorrectly assigning the<br>center of the system.</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">I would suggest re-building the system, starting from the editconf step, and<br>
centering the protein with -c in a box defined *either* by -d or -box, to see if<br>that fixes things.</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: AR-SA; mso-bidi-language: AR-SA">-Justin</span></div>
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> ------------------------------------------------------------------------<br>></span></div>
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