[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

Dear gmxusers,


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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