Hi priya ,<br><br> I am also have same problem...<br><br>From my limited experience ..<br><br>To solve these problem it is a good way to make <br>index file of particular group (or molecule ) <br>and then measure there g_mindist, g_gyrate and g_hbond <br>
You can get gyrate and hbond value for them...<br>Have a nice Day ...<br><br><br>With Best Wishes,<br>Ram<br><br><br><div class="gmail_quote">On Mon, Apr 9, 2012 at 6:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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>
priya thiyagarajan wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
hello sir ,<br>
<br>
i got few basic doubts in dynamics..<br>
<br>
while performing analysis, we are calculating rmsd and gyrate for single molecule..<br>
<br>
but in case of more molecules i.e by adding 20 molecules randomly using genbox , when we perform analysis, rmsd value we are obtaining is the average change in structure deviation from initial structure.<br>
<br>
what about gyrate??<br>
<br>
i am getting one plot... how to interpret the result for 20 moecules..since 20 molecules arranged randomly, how it calculates the gyrate value..<br>
<br>
please help me with your answer..<br>
<br>
</blockquote>
<br></div></div>
I think g_polystat is more appropriate in this case.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
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