[gmx-users] From one lipid molecule to a bilayer?

David spoel at xray.bmc.uu.se
Thu Nov 6 07:47:00 CET 2003

On Thu, 2003-11-06 at 05:54, Zhen Qin wrote:
> Dear gromacs users,
>  I have a question. I got the PDB file for one lipid molecule. Now I need
> to construct a bilayer with that? Can gromacs do that? Does anybody have
> any experience with that?
yes, but it will take time equilibrating.

align the lipid along the z axis of a box:
editconf -princ (maybe you need to rotate it around an axis afterwards)
make an arrangement in a plane:
genconf -nbox 8 8 1
scale the box to the right area per headgroup
editconf -scale X Y Z

add water (genbox)

do energy minimization

do restrained molecular dynamics where you leave fix e.g. the phosphor

do free MD
> Thanks.
> -Zhen
> Have a good day !  ^&^
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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