[gmx-users] lipid gel phase simulation model building

[Justin A. Lemkul]

Quoting Carsten Selle <selle at physik.uni-leipzig.de>:

> 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.

You might find some useful information here:

http://wiki.gromacs.org/index.php/Membrane_Simulations

-Justin

>
> Best regards,
> Carsten
>
> --
>
> Dr. Carsten Selle
> University of Leipzig
> Institute for Experimental Physics I
> PWM
> Linnestr. 5
> D-04103 Leipzig
> Germany
>
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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