A building block of the SBCG lipid model consists of two beads - a ``head" bead and a ``tail" bead - connected by a harmonic bond. This is the simplest representation that preserves the elongated shape of a real lipid molecule as well as the separation of hydrophobic and hydrophilic parts. Even so, if we were to represent a single all-atom lipid, which contains less than 150 atoms, in this way, the resulting beads would be too light to accommodate the long timesteps desired in a SBCG simulation. We therefore have to view SBCG lipid ``molecules'' in a more abstract sense, allowing that one SBCG ``molecule'' represents a small patch of all-atom lipids, rather than one real all-atom lipid molecule.
At this level of coarse-graining, the differences between lipids of different types (e.g. POPE vs. POPC or DOPC) become almost negligible. However, SBCG lipids can be matched to all-atom simulations by considering qualities such as the bilayer thickness and area per lipid. Since the lipid bilayer thickness is approximated to be 50 Å, each bead therefore has a diameter of 12.5 Å. One SBCG lipid occupies then a cross-sectional area of approximately 156 Å. In this tutorial, we will be working mainly with DOPC, which occupies 72.5 Å per lipid. One SBCG DOPC lipid must then represent approximately 2.2 all-atom DOPC lipids. The mass of the 2.2 lipids is divided equally among the ``head" and the ``tail" beads, meaning that the ``head" bead actually represents both the head groups of the lipids and some portion of the tails, and the ``tail" bead represents the remainder of the lipid tails. Since one DOPC lipid contains 138 atoms, 2.2 lipids corresponds to 300 atoms, or 150 atoms per SBCG bead, consistent with the level of coarse graining used for the BAR domain proteins. In many circumstances, one will want to include charged as well as neutral lipids. We therefore will also define negatively charged SBCG lipids to represent DOPS to use in a mixed DOPC/DOPS membrane. Since DOPC is the main lipid, and we have already determined that one SBCG lipid represents 2.2 all-atom lipids, this convention is kept for DOPS. Since DOPS is slightly heavier, the extra mass is added to the DOPS ``head" bead so that the ``tail" beads of the two lipids can remain identical. The DOPS ``head" bead is given a charge of -2.2 to account for the fact that it incorporates 2.2 all-atom DOPS lipids. All these characteristics are reflected in the provided topology file for SBCG lipids, 3_cg_membrane/lipid-ion.top.
The bond parameters and nonbonded parameters for the SBCG lipids were chosen to consistently reproduce the bilayer thickness and area per lipid values in all-atom simulations, as described in detail in Arkhipov et al., Biophys. J., 95:2806, 2008. Since we do not run simulations in this section, a parameter file is not necessary at this point. We will need the parameter file later, when we run a CG simulation of a combined lipid-protein system.
2. To create a corresponding psf file, use the provided psfgen script 3_cg_membrane/build-dopc.tcl by typing the following into the Tk Console:
3. One may alternatively use the AutoPSF plugin in VMD to create a psf file. To do this, navigate to Extensions Modeling Automatic PSF Builder. In Step 1, check that dopc.pdb is set as the input molecule, and set the desired output file name. Under ``topology files'' delete the default all-atom topology and then add the SBCG topology file lipid-ion.top by clicking ``Add'' and selecting lipid-ion.top. In Step 2, Select ``Everything'' and click ``Guess and split chains using current selections''. In Step 3, click ``Create Chains" to create the psf file.
4. Load the resulting pdb and psf files into VMD. You should see a 37 9 array of SBCG lipids.
We will now create a combined DOPC/DOPS membrane by changing some of the DOPC lipids to DOPS. The provided script 3_cg_membrane/mutate-to-dops.tcl selects 30% of the lipids at random and changes them to DOPS.
1. To use this script, type the following into the Tk Console:
2. Now create a psf file either by using the provided psfgen script 3_cg_membrane/build-mixture.tcl by typing
or by using the AutoPSF plugin.
3. Load the resulting pdb and psf files into VMD - you should see that about 30% of the lipids are now DOPS lipids. For example, you can color lipids by resname to distinguish between DOPC and DOPS.
You will need this mixed DOPC/DOPS membrane patch for the simulations in following sections.