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

[David]

On Thu, 2003-11-06 at 21:07, Zhen Qin wrote:
> 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?
with editconf and genconf
> 
> -Zhen
> 
> 
> 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
> > atom
> >
> > do free MD
> > >
> > > Thanks.
> > >
> > > -Zhen
> > >
> > > Have a good day !  ^&^
> > > _______________________________________________
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> > --
> > David.
> > ________________________________________________________________________
> > 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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-- 
David.
________________________________________________________________________
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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