<div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Apr 27, 2012 at 7:37 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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="im"><br>
<br>
On 4/27/12 10:00 AM, Bala S wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Anirban,<br>
<br>
Exactly.. That's the gap (either side of the leaflets) I was mentioning<br>
about. I'll try EM and check itagain.<br>
<br>
</blockquote>
<br></div>
EM won't fill in solvent gaps. If you're using my protocol for increasing the C radius in vdwradii.dat, then a small gap is normal and will close when doing equilibration as the solvent fills in around the lipid headgroups.<div class="im HOEnZb">
<br></div></blockquote><div> Yes, as Justin mentioned, the equilibration runs (restraining the protein) will fill those gaps.</div><div><br></div><div>Anirban</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im HOEnZb">
-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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==============================<u></u>==========<br></div><div class="HOEnZb"><div class="h5">
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