[gmx-users] Energy Minimization with Lipid Bilayer

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Mon Nov 20 12:46:17 CET 2006

> I am having a problem with energy minimization of a DPPC bilayer and  
>  solvent.  I
> have searched the archives for a good long while to help solve my   
> problem, but
> so far I have had no luck.  The system I am building consists of the bilayer
> and solvent molecules (water), in preparation for the insertion of a membrane
> protein.  I have successfully done energy minimization on the bilayer with
> crystal waters.

If this bilayer is in the crystalline state, as you refer to "crystal  
waters", then I think the problem lies exactly there.
Of course you are interested in the liquid-crystalline state, as long  
as you are adding waters to solvate the bilayer. In that case I  
suggest you to increase the area per lipid, even before you minimize  
the energy.
A simulated bilayer system  with a "wrong" area per lipid may cause a  
great increase in the Pxx/Pyy components of the pressure tensor  
(hundreds or even thousands of atm!).



Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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