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<p class="MsoNormal">Hi Eric,</p>
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<p class="MsoNormal">Thank you very much for your help. Although I am not sure whether is the university or the mailing list blocked the code content. Nevertheless, I appreciate your help.
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<p class="MsoNormal">Best regards,</p>
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<p class="MsoNormal">Ben</p>
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<p class="MsoNormal">Ph.D, M.Eng, FHEA</p>
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<p class="MsoNormal" style="border:none; padding:0cm"><b>From: </b><a href="mailto:pett@cgl.ucsf.edu">Eric Pettersen</a><br>
<b>Sent: </b>24 April 2020 02:51<br>
<b>To: </b><a href="mailto:benjamintam@um.edu.mo">benjamintam</a><br>
<b>Cc: </b><a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
<b>Subject: </b>Re: [Chimera-users] Imagine processing from gromacs</p>
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<div>Hi Ben,
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Typically, one “wraps” a PBC trajectory to produce a new trajectory where molecules stay whole on one side of the box or the other. For Gromacs, the tool for that is trjconv, perhaps
with the “-pbc whole” flags. See this page: <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__manual.gromacs.org_documentation_2018_onlinehelp_gmx-2Dtrjconv.html&d=DwMFaQ&c=KXXihdR8fRNGFkKiMQzstu-8MbOxd1NuZkcSBymGmgo&r=EElAJhvpEXZIOG4aO3Q_1Fg1wh-iIcDTLJ2t8QVMlxU&m=pJfYo02dBWyMImWhNt9SQhEshAF42kEnCABBWjH3NjM&s=Vfw1MLZfC1pHcWEsIFazzl3tZ-0l-fHmOMBi6IeaOBs&e=" class="">gmx
trjconv — GROMACS 2018 documentation</a>.</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>If wrapping a trajectory is problematic for some reason, you could define a per-frame Python script to hide long bonds. I have attached such a script. To use it, in the MD Movie GUI
choose the Per-Frame→Define script… menu entry, and in the resulting dialog change the script type to “Python” and use the “Insert text file” button near the button to insert the attached Python file. Then click OK. Long bonds should disappear and you can
play your trajectory and bonds will be hidden and shown appropriately.</div>
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<div class="">--Eric</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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