[gmx-users] generation of bilayer structures

Javier Cerezo jcb1 at um.es
Thu Jun 10 18:14:57 CEST 2010

Hi all.

I am trying to build up a bilayer consisting of a lipid (i.e. DMPC) and 
a fatty acid. Although I've seen some biblio related with this topic, 
the methodology about how to insert the fatty acid chain into an 
equilibrated bilayer is not so clear for me. In J. Phys. Chem. B 2009. 
113, 92-102, it is suggested that the fatty acid chains could be 
inserted using tlc scripting withing VDM, but no clue about the 
insertion algorithm itself.  So I tried the following (using fortran 
code): first locate the "best" positions to place the fatty acid chain 
and subsequently placing them and expanding the cell a bit (by a factor 
of 1.2) to ensure place enough for the inserted chains. Then the are 
rotated along z-axis to find the best orientation. Subsequent 
minimization, solvation and equilibration (NPT) should yield an optimal 
starting structure for production, but I am not entirely satisfied with 
the result (sometimes it works, sometimes the systems crashes mainly due 
to problems during communication between nodes). So I wonder if someone 
of you has an idea about an efficient way to generate lipid bilayers 
that may work for my problem.

In addition, I would like to know how Gromacs handles the coordinates 
out of the simulation box in the .gro file during a simulation. I guess 
it just replicate the coordinates inside the box by the opposite face 
(using PBC) but I would like to have comment about it if you know.

Thanks a lot!


Estudiante de Doctorado
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)

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