We will do 3_membrane in the tutorial files
In popc128_700ns, I uploaded a 700-ns simulation of a POPC bilayer system.
all.1ns.xtc: 700-ns trajectory with 1-ns time step.
You can generate your own membrane system using CHARMM-GUI web server.
topol.top looks like this:
The major difference between water box and membrane box is the pressure coupling part.
Membrane is not isotropic. Most natural choice for memrbane is semi-isotropic pressure coupling (Pxx = Pyy and Pzz are independent).
By setting Pxx = Pyy = 1 bar and Pzz = 1 bar, we can simulate zero surface tension.
Spatial distribution of lipid and water
Using all.1ns.xtc trajectory file, we can characterize the spatial distributions of water and lipid molecules along the normal direction.
gmx density is the program for this purpose.
-d Z: density as a function of z. In other words, average over xy plane.
-dens mass: mass density.
-sl 30: the number of slices along the z axis.
-ng 2: the number of groups for analysis.
The membrane has a hydrophobic core of ~3 nm width that has no water molecules at all.
What is the chance that a water molecule crosses the membrane?
We can answer that by calculating ∆G using the umbrella sampling and WHAM.
Diffusion of water and lipid
Using all.1ns.xtc trajectory file, we can compare the diffusion coefficients of water and lipid molecules.
Obviously, water diffusion is much faster.
Homework: calculate the diffusion coefficients of water and lipid by using gmx msd.
Umbrella sampling of a water molecule as a function of the z-position
In the ∆G calculation for a water-water pair, the reaction coordinate was the distance between the water pair.
In this case, the reaction coordinate is the z-position of a water molecule with respect to the center of mass of the membrane.
First, we need to generate the index file
We will just select the first water molecule. The selection will not change the results. All water molecules are equal!
There are 128 POPC molecules. Thus, the residue index of the first water molecules will be 129.
Caution: The initial distance between chosen water molecules must be smaller than half of the box. Otherwise, it violated PBC.
The groups will look like this:
Perform simulation in each window
10 Å window
See PULL section in pull.10.mdp
Generate pull.10.tpr for gmx mdrun
-t state.cpt: use information from the check point file.
Perform MDRUN for 1 ns
pullx files contain the length of spring
pullf files contain the force on the spring (F = -kx)
Repeat same things for other windows. For example, 0, 2, 4, 6, 8 , 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34 Å
It will take much longer than the water box. Adjust the simulation time considering your computer.