<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Thanks.</span></div><div><span>I read that it doesn't matter if the protein moves and even protrudes the box. It's OK, but there is a question here; why doesn't the box move rather than the protein? <br></span></div><div><span>Is it possible for box to be defined every step?, then the protein would stay in the center of the box.<br></span></div><div><span></span></div><div> </div><div>Sincerely,<br>Shima<br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for
GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, June 14, 2012 12:22 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] protein near the edges of simulation box<br> </font> </div> <br>
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On 14/06/2012 5:47 PM, Shima Arasteh wrote:
<blockquote type="cite">
<div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;">
<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 http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions<br>
<br>
Mark<br>
</div>
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