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<p class=MsoNormal>Dear gmxusers,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am trying to make a lipid bilayer with specific dimensions
using gromacs. So far, I have got up to:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Download a lipid POPC128a.pdb from Peter Tieleman’s
website<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Use genconf –f popc128a.pdb –o popcx2.pdb –nbox
2 2 1 to multiply the lipid in the x and y axis. The
resultant output was a lipid with box vectors 12.478 , 12.359 and
6.919 (nm)<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>My ultimate aim is to generate a POPC bilayer with the dimensions
9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I
would like to “crop” the excess lipids to the required size if at
all possible. I tried using editconf ( a bit of a long shot) to make a new box
size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000
but when I view it with VMD, it is not any smaller than before.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Do I have to use other software to achieve this? If so, I’d
really appreciate some pointers.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks!<o:p></o:p></p>
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