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<div>Hi</div>
<div>From the Gromacs Manual, </div>
<div><a href="http://manual.gromacs.org/current/online/editconf.html">http://manual.gromacs.org/current/online/editconf.html</a></div>
<div>editconf =></div>
<div>The box can be modified with options <tt>-box</tt>, <tt>-d</tt> and <tt>-angles</tt>. Both <tt>-box</tt> and <tt>-d</tt> will center the system in the box. </div>
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<div>so, without -c option, the protein is already centered in the box.</div>
<div>and, there is no description in the manual that people cannot use -d and -box simultaneously. </div>
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<div>I visualized the .gro file created by the editconf, the protein is centered in the box as I can see.</div>
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<div>Thank you</div>
<div>Lin</div>
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<div><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.</div>
<div>Mark already pointed out that your command line is malformed. You 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.</div>
<div>I would suggest that you at least try rebuilding your system, because the above<br>command is certainly wrong.</div>
<div>-Justin</div>
<div>> Thank you<br>> Lin</div>