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On 14/06/2012 5:47 PM, Shima Arasteh wrote:
<blockquote
cite="mid:1339660049.64436.YahooMailNeo@web36402.mail.mud.yahoo.com"
type="cite">
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<div><span>Dear gmx friends,</span></div>
<div><br>
<span></span></div>
<div><span>I put a protein in a simulation box filled of water
molecules and entered the mdrun command. After the
simulation, I found the protein near one of the edges of the
box and not in center. What is the problem? Anyone may
suggest me? <br>
</span></div>
<div><span>Does it mean that the simulation is meaningless? <br>
</span></div>
<div><span>I expect the protein to stay in the center of box and
goes unfold by passing the time.<br>
</span></div>
<br>
</div>
</blockquote>
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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