[gmx-users] How to make a lipid bilayer with specific dimensions?
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Mon Sep 27 05:09:34 CEST 2010
I am trying to make a lipid bilayer with specific dimensions using
gromacs. So far, I have got up to:
1) Download a lipid POPC128a.pdb from Peter Tieleman's website
2) 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)
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.
Do I have to use other software to achieve this? If so, I'd really
appreciate some pointers.
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