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On 25/10/2011 5:29 PM, James Starlight wrote:
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This was due to that in .gro file corresponded to the end of
productive MD I've found this <a moz-do-not-send="true"
href="http://i1209.photobucket.com/albums/cc394/own11/mdL.png">http://i1209.photobucket.com/albums/cc394/own11/mdL.png</a><br>
It's looks like the protein moved out from box so I've thought
that some error occured during stimulation<br>
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There's no outside to a periodic cell - you will find a matching
cavity on the other side of the triclinic periodic cell, where some
of the solute atoms actually are also.... <br>
<br>
GROMACS uses the triclinic representation internally for efficiency
- a 2D analogy is that a hexagon tiling a plane can be converted to
a rhombus tiling the plane. It doesn't bother wasting your valuable
computing cluster time converting back to the initial
representation, which probably wasn't wanted. That is, mdrun makes
no attempt to guess how you would like your output to appear. See <a
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a>
for ideas about how to make your output look as you would like.<br>
<br>
Mark<br>
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I don't understand this statement. You should also note that
a periodic box has no "outside." Perhaps it would be useful
to post images online. If you choose to do so, please follow
bullet point #4 here:<br>
<br>
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-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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