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On 30/01/2012 4:54 PM, Kowsar Bagherzadeh wrote:
<blockquote
cite="mid:1327902882.21403.YahooMailNeo@web161505.mail.bf1.yahoo.com"
type="cite">
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<div style="RIGHT: auto">Dear gmx-users,</div>
<div style="RIGHT: auto"> </div>
<div style="RIGHT: auto">Running MD, I faced a problem, after
1ps of modeling, the box changes its shape
from dodecahedron to rhomboid cube! and as a result some
parts of the protein gets out of the box. I fixed it with
trjcon command but keep comming up. Would you mind telling me
where this problem arise from?!</div>
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<br>
This sounds like normal behaviour. See <a
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>
<br>
Mark<br>
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