thanks for your reply<br><br>i have got output file,i used the following options:<br># g_order -f md.xtc -s md.tpr -n sn1.ndx -o order-sn1.xvg -od deuter-sn1.xvg -d z<br><br>whatever deuter-sn1.xvg get me is the same Sc-c (the vector Ci-1,Ci,Ci+1 is considered as molecule vector)? where i used the united atoms force field for my system.<br>
<br>thanks very much,<br>Afsaneh<br><br><div class="gmail_quote">On Sun, Feb 7, 2010 at 7:14 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
afsaneh maleki 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 all,<br>
<br>
i used united the atom force field model for the membrane lipids . to calculate order parameter i used :<br>
g_order -od -d<br>
i know united atom force field doesn't have hydrogen atoms in hydrocarbons chains .<br>
i want to know gromacs calculates order parameter * Sc-c* or *Sc-d* (Deuterium) ?<br>
</blockquote>
<br></div>
Simple geometry.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
in the output is written: title "Deuterium order parameters"<br>
<br>
</blockquote>
<br></div>
Is that it? If you've got an empty output, then your index file probably wasn't prepared correctly. There is a how-to on the g_order page on the Gromacs website:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order" target="_blank">http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order</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;">
thanks in advance,<br>
Afsaneh<br>
<br>
</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>
<br>
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