<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br>Hello anahita,<br><br><br>use pbc in your simulation.<br><br><br><br>regards,<br>Ravi <br><div><br><span style="color: rgb(56, 83, 118); font-family: comic sans ms;"></span><span style="color: rgb(56, 83, 118); font-family: comic sans ms;"><br> <br></span></div><br><br>--- On <b>Fri, 1/4/11, anahita <i><ana_j0000@yahoo.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: anahita <ana_j0000@yahoo.com><br>Subject: [gmx-users] FW:
protein split over boundary<br>To: "'Discussion list for GROMACS users'" <gmx-users@gromacs.org><br>Date: Friday, 1 April, 2011, 10:53 AM<br><br><div id="yiv2045046912">
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<p class="yiv2045046912MsoNormal"><b><span style="font-size: 10pt; font-family: "sans-serif";">From:</span></b><span style="font-size: 10pt; font-family: "sans-serif";"> anahita
[mailto:ana_j0000@yahoo.com] <br>
<b>Sent:</b> Friday, April 01, 2011 1:13 PM<br>
<b>To:</b> 'gmx-users-request@gromacs.org'<br>
<b>Subject:</b> protein split over boundary</span></p>
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<p class="yiv2045046912MsoNormal">Dear user,</p>
<p class="yiv2045046912MsoNormal">Hello, I appreciate if somebody help me. During the
simulation of my protein I didn’t get any error but after 1ns of MD</p>
<p class="yiv2045046912MsoNormal">my molecule was split over boundary in cubic box. it means
some part of it enter the other side of the box.</p>
<p class="yiv2045046912MsoNormal">At first,For decreasing the cost of simulation, in
“editconf” command I set the number “d” on 0.9 to decease the box size. I
want to mention that during the calculation my rvdw is 1.4.</p>
<p class="yiv2045046912MsoNormal">I want to know instead of problem of visualization, the
other things is fine?</p>
<p class="yiv2045046912MsoNormal">Best regards.</p>
<p class="yiv2045046912MsoNormal">A. johari</p>
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