Justin,<br><br><br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
I don't need the files. I'm just trying to save you time. If I want to see a coordinate file, I'll ask for it to be sent to me directly. I have seen no such need yet.</blockquote><div><br>Ok.<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;">
Application of pressure causes the box to change. The water won't leak in during NVT because the components of the system are trying to keep the box full since its dimensions are invariant.
Such leakage is typical during equilibration, as I've said. You should not be alarmed by this result.</blockquote><div>So presence of several water molecules within the membrane after equilibration will not cause futher errors in simulation, won't it? After 1 ns MD simulation of my system I've found that some waters were excluded from the bi-layer.<br>
<br>By the way the system prepared by G_membed consisted of more water molecules within the membrane after solvation via Genbox ( I've used vdv radius of 0.5 for carbons ). <br><br><br>Finally, I'd like to analyse results obtained after 1ns simulation. Firstly I want to compare some physical values of my system with the experiment. I found that I can analyse some such parametries like A per lipid ( I've already known this experimental value) as well as <font face="Arial"><font size="3"><b>Density of the Membrane and the coefficent of the </b></font></font><font face="Arial"><font size="3"><b>Lateral Diffusion for Lipids. Where I could found last two experimental values for my system as well for other lipids?<br>
<br><br><br>James<br></b></font></font></div><div><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;"><div><div class="h5">
<br>
-Justin<br>
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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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