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<div>Hi</div>
<div>Tsjerk gave me suggestion to check the .tpr file created by the command grompp.</div>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><b style="mso-bidi-font-weight: normal"><span lang="EN-US" style="COLOR: red"><font size="3"><font face="Times New Roman">Energy minimization of the solvated system</font></font></span></b></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US" style="BACKGROUND: yellow"><font size="3"><font face="Times New Roman">pbc = xyz (minim.mdp)</font></font></span></p>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3">grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated </font></span></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><span lang="EN-US"><font face="Times New Roman" size="3">mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated </font></span></p>
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<div>I early prepared for <font face="Times New Roman"><strong>6LYZ-solvated.gro</strong> and then run the command grompp to create 6LYZ-EM-solvated.tpr.</font></div>
<div><font face="Times New Roman">Next, run the command <strong>editconf -f </strong></font><strong>6LYZ-EM-solvated.tpr -o 6LYZ-EM-solvated-after-grompp.gro</strong></div>
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<div>Use, VMD to visualize both <font face="Times New Roman"><strong>6LYZ-solvated.gro</strong> and </font><strong>6LYZ-EM-solvated-after-grompp.gro</strong></div>
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<div><font face="Times New Roman"><strong>6LYZ-solvated.gro => all molecules are intact </strong> and protein is centered.</font></div>
<div><strong>6LYZ-EM-solvated-after-grompp.gro => protein and water molecules are broken.</strong></div>
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<div>This is the main problem that my simulation box into 16 domains.</div>
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<div>Thank you</div>
<div>Lin</div>
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<div><br>Chih-Ying Lin wrote:<br>><br>> Hi<br>> From the Gromacs Manual,<br>> <a href="http://manual.gromacs.org/current/online/editconf.html">http://manual.gromacs.org/current/online/editconf.html</a><br>> editconf =><br>
> The box can be modified with options -box, -d and -angles. Both -box and<br>> -d will center the system in the box.<br>><br>> so, without -c option, the protein is already centered in the box.<br>> and, there is no description in the manual that people cannot use -d and<br>
> -box simultaneously.<br>></div>
<div>The manual cannot possibly warn against everything that people may try to do.<br>Consider the function of these two options. By using -d, editconf will<br>determine a suitable box size based on the dimensions of the solute. By using<br>
-box, you are specifying the box vectors, which completely negates the purpose<br>of using -d. Perhaps the language in the manual is not clear. Both -d and -box<br>may center the solute, but *not* by simultaneously using -box and -d, because<br>
they can counteract each other. In the absence of a warning, something odd<br>might be going on; we must eliminate this possibility in order to help you better.</div>
<div>I would still suggest using a properly-formed command, with or without -c, to<br>make sure that nothing is breaking down there. The workflow you posted before<br>seems reasonable enough, so something early on is probably breaking down. Is<br>
there any reason you minimized your protein without PBC? What was the box size<br>used in this EM step? Usually an in vacuo EM is simply accomplished by using a<br>huge box and plain cutoffs. Solution EM would use a suitable box (with editconf<br>
-d *or* editconf -box) and better electrostatics methods.</div>
<div>-Justin</div>
<div>> I visualized the .gro file created by the editconf, the protein is<br>> centered in the box as I can see.<br>><br>> Thank you<br>> Lin<br>><br>><br>><br>><br>><br>><br>> Chih-Ying Lin wrote:<br>
> ><br>> ><br>> ><br>> > Hi<br>> > As I posted the command list earlier, to create the box<br>> > editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75<br>> > -box 6.0 6.0 6.0<br>
> ><br>> ><br>> > So, I think Justin's case is not the same as mine.<br>> Mark already pointed out that your command line is malformed. You<br>> cannot use -d<br>> and -box simultaneously. They are mutually exclusive. You are also not<br>
> centering the protein in the box (you are not using the -c option). So, in<br>> fact, what you're doing was exactly what my problem was - not centering and<br>> potentially defining the box incorrectly.<br>
> I would suggest that you at least try rebuilding your system, because<br>> the above<br>> command is certainly wrong.<br>> -Justin<br>> > Thank you<br>> > Lin</div>