anyone ? :)<br><br><div class="gmail_quote">On Fri, Jul 22, 2011 at 1:19 PM, maria goranovic <span dir="ltr"><<a href="mailto:mariagoranovic@gmail.com">mariagoranovic@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi<div><br></div><div>I am trying to calculate angle between helices using g_bundle and:</div><div><br></div><div><a href="http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html</a></div>
<div><br></div><div><a href="http://lists.gromacs.org/pipermail/gmx-users/2007-October/030415.html" target="_blank"></a>I am unable to understand how the -na option works. "the program reads 2 index groups and divides them into na parts". I will use -na 2 for 2 axes. But what should the index groups be? with -na 1 I would use the CA atoms on the top and bottom of the helix as the 2 index groups. For 2 helices, should the first index group be the CA atoms at the beginning of the 2 helices? Or should the first index group contain top and bottom CA atoms on the same helix, and the second index group should contain the same for the second helix?</div>
<div><br></div><div>Thank you for clarifying</div><div><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
</div>
</blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>