<br>Thank you Justin,<br><br>indeed it's pbc = xyz in my md.log file.<br><br>Carla<br><br><div class="gmail_quote">On Fri, Feb 25, 2011 at 3:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<br>
Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi everyone,<br>
<br>
In my .mdp MD file, I didn't put "pbc =xyz". Then, I used tpbconv and mdrun to continue my simulation.<br>
<br>
My question is: did I run my simulation using periodic boundary conditions because I have the impression that I did but I'm not sure if not using the mention "pbc" in my mdp file means that I didn't use PBC?<br>
</blockquote>
<br></div></div>
pbc=xyz is the default if not specified. Check your mdout.mdp and md.log files to be sure.<br>
<br>
-Justin<br>
<br>
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<br>
Thanks<br>
<br>
Carla<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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