Thank you! I will find out!<br><br><div class="gmail_quote">On Tue, Jun 12, 2012 at 3:41 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
On 6/12/12 10:39 AM, Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gmx Users,<br>
<br>
Do I have to get rid of pbc from my trajectory in order to calculate number of<br>
hydrogen bonds using g_hbond? I mean: Does pbc has any influence on the number<br>
of hydrogen bonds?<br>
<br>
</blockquote>
<br></div></div>
Nearly all Gromacs analysis tools deal with periodicity. g_hbond only needs to measure simple distances and angles, which should be unaffected by PBC. Try it and see.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br>
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Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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</font></span></blockquote></div><br>