Hi Kirill,<div>Although I can't directly address your question, I came across some recent work dealing with depth of penetration in lipid bilayers. May be the authors could help you.</div><div><a href="http://www3.interscience.wiley.com/journal/122351396/abstract">http://www3.interscience.wiley.com/journal/122351396/abstract</a></div>
<div><a href="http://www3.interscience.wiley.com/journal/122351396/abstract"></a>Hope this helps.</div><div>Pavan<br><br><div class="gmail_quote">On Wed, Dec 23, 2009 at 11:27 AM, Kirill Bessonov <span dir="ltr"><<a href="mailto:kbessonov@gmail.com">kbessonov@gmail.com</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">Dear gromacs pros,<br><br>I need to calculate depth of DMPC bilayer penetration by my 14 aa long peptide. I'm not sure how to do it, but I have tried g_dist program and calculated distance between DMPC and peptide groups for every frame of simulation. Is that correct way of doing it or maybe there is a better way? I've got xvg file. First column is time and second is distance in Amstrongs?<br>
<br></div>Thank you<br>
<br>--<br>
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