[gmx-users] lipid gel phase simulation model building

[chris.neale at utoronto.ca]

> Dear gromacs users,
>
> the gel phase of some lipids as the L beta prime of DPPC is
> characterized by all-trans alkyl chains which are tilted with respect to
> the bilayer normal. I would like to set set up a system analog to the
> one described by Venable, Brooks & Pastor, J. Chem. Phys., 112 (2000),
> pp. 4822. They used a periodic box which is cubic (39 x 39 x 63 A***3).
> I tried editconf and genbox to  generate a cubic simulation box and a
> suitable aqueous environment for the bilayer I generated from crystal
> data. However, since the box is cubic, there is plenty of room for
> unwanted water-alkyl interaction. genbox accordingly placed water in
> hydrophobic places.  The water molecules should (almost) only interact
> with with the lipid headgroups and water. Any helpful comment is greatly
> appreciated.
>
> Best regards,
> Carsten

Try keepbyz.sh at http://wiki.gromacs.org/index.php/Membrane_Simulations

Also note that, assuming your membrane normal is along z, editconf  
will make the box bigger than you would like in the xy plane since it  
probably doesn't fit perfectly by PBC and water will come in (at the  
sides especially) during initial equilibration. If your gel really  
does do PBC already then try just cutting down the x and y and  
checking it out via g_mindist to ensure the crash is not too bad in a  
trial-and-error process. You could also try inflategro from the  
Tieleman lab without using a protein and that may help you get the  
sides, although I am not sure that this would work as expected.

Chris.