[gmx-users] lipid gel phase simulation model building

[Marc F. Lensink]

On Thu, May 29, 2008 at 06:27:00PM +0200, Carsten Selle wrote:
> 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.

perhaps your box is too large in the xy-direction?  shorten it and try
again until it's okay.  you can avoid water placement inside the
bilayer by setting a van der waals radius of 0.35 or so on those
carbons.

you can also try a different approach: i recently took an equilibrated
popc bilayer, saturated the double bond and added 2 carbons to the
sn-1 chain (the shorter one).  after some equilibration the system
tightened to gel phase within 10 ns of simulation.  20 degree tilt, by
the way.

cheers,
marc


-- 
Marc F. Lensink
Centre for Structural Biology and Bioinformatics          CSBB
Université Libre de Bruxelles           marc.lensink at ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425