<div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Apr 27, 2012 at 6:31 PM, Bala S <span dir="ltr"><<a href="mailto:think_beyond@aol.com" target="_blank">think_beyond@aol.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<br>
OOPS!!<br>
Sorry for that.. Now I could realize it.<br>
Following up.. I have done further iterations with inflategro and reached<br>
0.62 nm^2 which similar to what you have explained in the tutorial.<br>
<br>
Now, I could see the lipid bilayer really shrinked and no SOL molecules are<br>
seen in between. Now the issue I would like to have clarification on is that<br>
only 163 SOL molecules were added up and down which looks very scarce for<br>
the simulation.<br>
<br>
What is the solution?<br>
<br></blockquote><div><br></div><div>First visualize and see whether the hydrophilic ends of the lipid bilayer and your protein's part on either side of the bilayer (like a GPCR's intra and extra cellular ends) are well immersed in the water box. If not, you can increase the solvation box along the z-axis by increasing the z value for -box option in editconf (keeping x and y values same).</div>
<div><br></div><div>Anirban</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Bala S<br>
<br>
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