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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I’m using gromacs for MD simulations on membrane
proteins. As part of the analysis I would like to calculate the average
area per lipid. I’ve been going about this by pulling the
coordinates from the trajectory in VMD, then importing these to Mathematica and
using it to plot a voronoi tessellation. The problem I run in to is I
have to discard ~10% of the data (when averaging over multiple frames) due to
Mathematica not being able to complete the tessellation. I believe this
is occurring as a result of PBC and Mathematica plotting concave polygons. That
being said, I have just about given up on my method.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I was wondering if anyone out there has a script or
methodology they would be willing to share with me in order to calculate the
area per lipid with a protein present (i.e using a voronoi tessellation). I
would appreciate it tremendously!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Sincerely,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Stephen Dutz<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Department of Chemistry &<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Center for Macromolecular Modeling and Materials
Design <o:p></o:p></span></font></p>
<p class=MsoNormal><st1:PlaceName w:st="on"><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>California</span></font></st1:PlaceName><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> <st1:PlaceType
w:st="on">State</st1:PlaceType> <st1:PlaceName w:st="on">Polytechnic</st1:PlaceName>
<st1:PlaceType w:st="on">University</st1:PlaceType>, <st1:City w:st="on"><st1:place
w:st="on">Pomona</st1:place></st1:City><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><a href="http://www.csupomona.edu/~smdutz">http://www.csupomona.edu/~smdutz</a><o:p></o:p></span></font></p>
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12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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