[gmx-users] generation of bilayer structures
jcb1 at um.es
Thu Jun 10 18:14:57 CEST 2010
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!
Javier CEREZO BASTIDA
Estudiante de Doctorado
Universidad de Murcia
30100 MURCIA (España)
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