[gmx-users] From one lipid molecule to a bilayer?
Zhen.Qin at hec.utah.edu
Thu Nov 6 21:08:01 CET 2003
Thank you so much. But I think by doing so, you can only get one layer
of lipid. How do you get the bilayer with two layer?
Have a good day ! ^&^
On Thu, 6 Nov 2003, David wrote:
> 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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