start/mdRipple/experiment.tex

Our idea for developing a simple and reasonable lipid model to study
the ripple pahse of lipid bilayers is based on two facts: one is that
the most essential feature of lipid molecules is their amphiphilic
structure with polar head groups and non-polar tails. Another fact is
that dominant numbers of lipid molecules are very rigid in ripple
phase which allows the details of the lipid molecules neglectable. In
our model, lipid molecules are represented by rigid bodies made of one
head sphere with a point dipole sitting on it and one ellipsoid tail,
the direction of the dipole is fixed to be perpendicular to the
tail. The breadth and length of tail are $\sigma_0$, $3\sigma_0$. The
diameter of heads varies from $1.20\sigma_0$ to $1.41\sigma_0$.  The
model of the solvent in our simulations is inspired by the idea of
``DPD'' water. Every four water molecules are reprsented by one
sphere.


Spheres interact each other with Lennard-Jones potential, ellipsoids
interact each other with Gay-Berne potential, dipoles interact each
other with typical dipole potential, spheres interact ellipsoids with
LJ-GB potential. All potentials are truncated at $25 \AA$ and shifted
at $22 \AA$.


To make the simulations less expensive and to observe long-time range
behavior of the lipid membranes, all simulaitons were started from two
sepetated monolayers in the vaccum with $x-y$ anisotropic pressure
coupling, length of $z$ axis of the simulations was fixed to prevent
the shrinkage of the simulation boxes due to the free volume outside
of the bilayer, and a constant surface tension was applied to enable
the fluctuation of the surface. Periodic boundaries were used. There
were $480-720$ lipid molecules in simulations according to different
size of the heads. All the simulations were stablized for $100ns$ at
$300K$. The resulted structures were solvated in the water (about
$6$DPD water/lipid molecule) as the initial configurations for another
$30ns$ relaxation. All simulations with water were carried out at
constant pressure ($P=1bar$) by $3D$ anisotropic coupling, and
constant surface tension ($\gamma=0.015$). Time step was
$50fs$. Simulations were performed by using OOPSE package.
Revision:	3484
Committed:	Tue Jan 13 14:39:51 2009 UTC (15 years, 6 months ago)
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#	Content
1	Our idea for developing a simple and reasonable lipid model to study
2	the ripple pahse of lipid bilayers is based on two facts: one is that
3	the most essential feature of lipid molecules is their amphiphilic
4	structure with polar head groups and non-polar tails. Another fact is
5	that dominant numbers of lipid molecules are very rigid in ripple
6	phase which allows the details of the lipid molecules neglectable. In
7	our model, lipid molecules are represented by rigid bodies made of one
8	head sphere with a point dipole sitting on it and one ellipsoid tail,
9	the direction of the dipole is fixed to be perpendicular to the
10	tail. The breadth and length of tail are $\sigma_0$, $3\sigma_0$. The
11	diameter of heads varies from $1.20\sigma_0$ to $1.41\sigma_0$. The
12	model of the solvent in our simulations is inspired by the idea of
13	``DPD'' water. Every four water molecules are reprsented by one
14	sphere.
15
16
17	Spheres interact each other with Lennard-Jones potential, ellipsoids
18	interact each other with Gay-Berne potential, dipoles interact each
19	other with typical dipole potential, spheres interact ellipsoids with
20	LJ-GB potential. All potentials are truncated at $25 \AA$ and shifted
21	at $22 \AA$.
22
23
24	To make the simulations less expensive and to observe long-time range
25	behavior of the lipid membranes, all simulaitons were started from two
26	sepetated monolayers in the vaccum with $x-y$ anisotropic pressure
27	coupling, length of $z$ axis of the simulations was fixed to prevent
28	the shrinkage of the simulation boxes due to the free volume outside
29	of the bilayer, and a constant surface tension was applied to enable
30	the fluctuation of the surface. Periodic boundaries were used. There
31	were $480-720$ lipid molecules in simulations according to different
32	size of the heads. All the simulations were stablized for $100ns$ at
33	$300K$. The resulted structures were solvated in the water (about
34	$6$DPD water/lipid molecule) as the initial configurations for another
35	$30ns$ relaxation. All simulations with water were carried out at
36	constant pressure ($P=1bar$) by $3D$ anisotropic coupling, and
37	constant surface tension ($\gamma=0.015$). Time step was
38	$50fs$. Simulations were performed by using OOPSE package.