Hi Carla,<br><br>I did this using g_hbond by supplying an index file with only the 3 atoms involved in the individual bond I was looking at. <br><br>I got this printed to screen:<br><br>"Average number of hbonds per timeframe 0.998 out of 1 possible"<br>
<br>Although it is time consuming to do it for more than a few hydrogen bonds.<br><br>Oliver<br><br><br><div class="gmail_quote">On 11 October 2010 14:49, Carla Jamous <span dir="ltr"><<a href="mailto:carlajamous@gmail.com">carlajamous@gmail.com</a>></span> 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>I tried to analyze the H-bonds in my trajectory with g-hbond and I analysed the xpm and ndx file. But now I need to know the percentage of existence of each hbond during my trajectory. Is there a way to do it with a command line? Or is there a program (someone told me there are python programs for analysis of gromacs trajectories) to extract this information from the .xpm file?<br>
<br>Thank you.<br><br>Cheers,<br><font color="#888888">Carla <br>
</font><br>--<br>
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