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<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>Dear GROMACS
users</span></font><span dir=RTL></span><span lang=HE dir=RTL><span dir=RTL></span>,<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>I have been
trying to expand a membrane by a non-integer multiplier (for example X1.5). This
can be done using</span></font><span lang=HE dir=RTL><o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=2 face=Tahoma><span style='font-size:10.0pt;font-family:
Tahoma;font-weight:bold'>genbox -cs Membrane.gro -o Expanded_membrane.gro –<st1:address
w:st="on"><st1:Street w:st="on">box</st1:Street> 1.5</st1:address>X 1.5Y Z</span></font></b><b><font
size=2 face=Tahoma><span lang=HE dir=RTL style='font-size:10.0pt;font-family:
Tahoma;font-weight:bold'><o:p></o:p></span></font></b></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span lang=HE dir=RTL style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>This has worked
very good with <u>homogenous</u> membranes, and only very short equilibrium
times were required to re-equilibrate the membrane (~10-20ns).<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'>Now </span></font>I am trying to deal the same way with <u>heterogeneous</u>
membrane (POPG/POPE mixture, Mikko<span dir=RTL></span><span dir=RTL><span
dir=RTL></span> </span>Karttunen et. al). <o:p></o:p></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>When</span></font><span
dir=RTL></span><span dir=RTL><span dir=RTL></span> </span>trying to invoke the
above command to the POPG/POPE membrane I get a<span dir=RTL></span><span
dir=RTL><span dir=RTL></span> </span>membrane with different compositions of
lipids in the upper and lower<span dir=RTL></span><span dir=RTL><span dir=RTL></span>
</span>leaflets<span dir=RTL></span><span lang=HE dir=RTL><span dir=RTL></span>.<o:p></o:p></span></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>This happens (so
I suspect) because the arrangement of lipids in each leaflet is somewhat
different so that the molecules that "get' to be multiplied do not conserve
the <o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face=Arial><span style='font-size:12.0pt'>same ratio of
different lipids as in the original structure (which has ratio of 1:3 POPG/POPE).<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'>Is there a way to multiply the membrane by a <u>non-integer</u>
number AND somehow conserve the ratio of different lipid species too?<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'>Or at the very least, to have both upper and lower leaflets
identical after multiplication? (This, too, would help immensely).<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'>-Shay<o:p></o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'><o:p> </o:p></span></font></p>
<p class=MsoPlainText dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 color=black face=Arial><span style='font-size:12.0pt;
color:black'><o:p> </o:p></span></font></p>
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