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The aim of the first part is to create and study properties of coarse-grained models of lipid bilayer membranes. First, we will attempt to spontaneously self-assemble a DSPC bilayer and check various properties that characterize lipid bilayers, such as the area per lipid, bilayer thickness, P₂ order parameters, and diffusion. Next, we will change the nature of the lipid head groups and tails, and study how that influences the properties. Finally, there is a slightly more advanced exercise on how to parameterize a Martini CG model of diC18:2-PC, a PC lipid with a doubly unsaturated tail, based on an all-atom simulation.

The files for the first section can be downloaded here:

Unpack the archive. (It expands locally, so to keep things clean put it in a separate directory, e.g. LIPIDS.)

We will begin with self-assembling a DSPC (distearoyl-phosphatidylcholine) bilayer from a random configuration of lipids and water in the simulation box. First, create this random configuration of 128 DSPC starting from a single DSPC molecule:

genbox -ci dspc_single.gro -nmol 128 -box 7.7 7.7 7.7 -try 100 -o 128_noW.gro

Next, minimize the system...

grompp -f em.mdp -c 128_noW.gro -p dspc.top -maxwarn 10

mdrun -v -c 128_minimised.gro

...add 6 CG waters (i.e., 24 all-atom waters) per lipid...

   genbox -cp 128_minimised.gro -cs water.gro -o waterbox.gro -maxsol 768

...and minimize again (adapt dspc.top to reflect the water beads added to the system):

grompp -f em.mdp -c waterbox.gro -p dspc.top -maxwarn 10

mdrun -v -c minimised.gro