<br><br><div class="gmail_quote">On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan <span dir="ltr"><<a href="mailto:c.poojari@fz-juelich.de">c.poojari@fz-juelich.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<br>
<br>
I have protein completely inserted into lipid membrane and would like to study order parameter around the protein as well as away from the protein.<br>
<br>
For this I would like to slice my membrane into parts.<br>
<br>
I tried the following command:<br>
<br>
g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2<br>
<br>
The output i get from this is as same as the one where i dont use -sl 2 flag and it also doesnt show the different parts it has used for order parameter calculation.<br>
<br>
Please can I know how to slice my lipid membrane so that i can study order parameter for each part separately.<br></blockquote><div><br>It seems that the lipid around the protein is not fixed, it's slowly flow (fluid).<br>
<br>during some time interval, not exactly the same lipids around the protein. maybe another different group.<br>so here -sl 2 won't serve well for what you wanna test. <br> <br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Kind Regards,<br>
chetan<br>
<br>
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