Dear Justin,<br><br>Thank you very much.<br><br>best,<br>Olga<br><br><div class="gmail_quote">2010/11/29 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Olga Ivchenko wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Leila,<br>
<br>
I am also have a task to calculate H-bonds frequency through the over all trajectory in gromacs. Please can you send me Justin's script. If he does not mind.<br>
<br>
</blockquote>
<br></div>
I have several analysis scripts available to the public on my website:<br>
<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yours sincerely,<br>
Olga<br>
<br>
2010/11/29 leila karami <<a href="mailto:karami.leila1@gmail.com" target="_blank">karami.leila1@gmail.com</a> <mailto:<a href="mailto:karami.leila1@gmail.com" target="_blank">karami.leila1@gmail.com</a>>><div class="im">
<br>
<br>
Dear Mark and gromacs users<br>
<br>
thanks for your time and consideration.<br>
<br>
<br>
<br>
you said by multiplying the existence functions for hbonds between protein and water and the hbonds between water and DNA, then using Justin's script, I can obtain percentage each water medited hydrogen bond during trajectory. <br>
<br>
and also you said I need to create a corresponding index file too.<br>
<br>
I don't know where should I start for multiply two existence functions?<br>
<br>
please explain about it more.<br>
<br>
any help will highly appreciated.<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
-- <br>
Leila Karami<br>
Ph.D. student of Physical Chemistry<br>
K.N. Toosi University of Technology<br>
Theoretical Physical Chemistry Group<br>
<br>
<br>
<br>
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</div></blockquote>
<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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