SPICA: Surface Property fItting Coarse grAined model

Tutoriallipid membrane

Step 1. Prepare initial configuration

The initial configuration for MD simulation can be generated by various tools, such packmol, avogadro, and VMD plugins. In this step, we will introduce how to prepare an initial configuration of lipid membrane in both AA and CG description. Here we will use CGenConf and CHARMM-GUI to create CG PDB file and AA PDB file, respectively. Since our tools are based on the PDB file format, we focus on how to prepare the intial coordinate files in PDB format. In the next step, the CG PDB file generated by CGenConf will be converted to LAMMPS compatible input file using setup_lammps. While the AA PDB file prepared by CHARMM-GUI will be converted using a VMD plugin tool, named CG-it.

CG PDB file: Random configuration using CGgenConf (tool in MPDyn2)

CGgenConf is a tool provided within MPDyn2 software package. This is useful to generate a random initial configurations at CG level. There are two steps to make a random configuration within a simulation box.
  1. Make a molecular library
  2. Pack the molecules picked up from the library

Make a molecular library

First, we need to generate a library of molecular structures for the molecules containing multiple beads. (not like water particle) Here we take a DOPC as an example to generate the molecular library.

A directory, ./MolLib should be made, where the library files are generated. Then, conduct ~/MPDyn2/bin/GenCGconf
Required information shoud be given interactively.

 # Do you want to make a library for a molecule? [Y or N]
> Y
# How many molecular structures do you (want to) have in the library?
> 1000 When you DON'T need the molecular library, put any POSITIVE number
Arbitrary number should be written. For example, usually, the numbers within 1000-9999 should be enough. If it exceeds 10000, it gives error.
# Do you have have a reference structure for some components of the system? [Y or N]
> N Usually....
# Name of PARAMETER file = ?
> par_CG.prm Put "D" for a default choice, "~/CGparam/par_CG.prm"
# Name of TOPOLOGY file = ?
> top_CG.prm Put "D" for a default choice, "~/CGparam/top_CG.prm"
# Number of molecular species = ?
> 1 We only make a library of DOPC, so here just answer 1.
# Molecular names ? Give them in one line.
> DOPC
# Number of Atoms in a Molecule ? Give them in one line.
> 7 In SPICA-CG, DOPC is made by 7 beads, so that put 7.

Then, you will find 1000 configuration files in ./MolLib directory.

Pack the molecules picked up from the library

Next, we pack the generated library molecules in the simulation box. To do this, we again use GenCGconf. ~/MPDyn2/bin/GenCGconf

# Do you want to make a library for a molecule? [Y or N]
> N This time, we use the previously generated library files
# Do you have have a reference structure for some components of the system? [Y or N]
> N Again, usually put "N". If and only if you have a membrane structure beforehand, just put some water molecules in the simulation box, you may put "Y", but for now, simply put "N".
# Name of PARAMETER file = ?
> par_CG.prm Put "D" for a default choice, "~/CGparam/par_CG.prm"
# Name of TOPOLOGY file = ?
> top_CG.prm Put "D" for a default choice, "~/CGparam/top_CG.prm"
# Number of molecular species = ?
> 2 We want to generate the binary system of DOPC and water, and then put 2
# Molecular names ? Give them in one line.
> DOPC WAT
# Number of Molecules ? Give them in one line.
> 1296 3456
# Number of Atoms in a Molecule ? Give them in one line.
> 7 1
# Periodic Boundary Condition is used or not? [Y or N]
> Y PBC is usually used, so that 'Y'B
# Density { rho [g/cm^3] } or the size of the simulation box{ Lx, Ly, Lz [A] }?
> 1.0 Giving a single value, it will be understood as density**
Put the density [g/cm] or insert the cell size (Lx,Ly,Lz). If a sinble value is put, it is considered as a density value. Now put 1.0

This produces the random initial configuration in a cubic box; initial.crd and final.pdb. initial.crd is the file to be used in MPDyn. final.pdb is just a corresponding PDB file. The PDB file does not contain topology data, you may need a PSF file to visulize by vmd.

AA PDB file: Random configuration using CHARMM-GUI

CHARMM-GUI is a web tool, which generates initial coordinates for various systems. We use CHARMM-GUI to prepare initial coordinates of lipid membrane system in all-atom format.
  1. Visit CHARMM-GUI web site and go to "Bilayer Builder" (Input Generator-Membrane Builder-Bilayer Builder)

  2. Scroll down and click "Membrane Only System"

  3. Tick "Heterogeneous Lipid" and "Numbers of lipid components". Change other options if needed (i.e., Water thickness).

  4. For this tutorial, we will prepare DOPC lipid membrane. Expand "PC (phosphatidylcholine) Lipids". Input 64 for both "# of Lipid on Upperleaflet" and "# of Lipid on Lowerleaflet" of DOPC.

  5. Click "Show the system info" button. Then, "Calculated XY system Size" will appear.

  6. Proceed to next step by clicking "Next Step: Determine the System Size"

  7. This step determines how many ions will be included in the system. Since PC lipids are neutral, we will not include ions in the system. Scroll down and untick "Include Ions". Then, go to next step.

  8. A message about the ions and water box will appear. Go to next step.

  9. CHARMM-GUI will assemble lipid membrane and solvation box. This step will take a while.

  10. The inital configuration is ready now. Download the files by clicking "download .tgz" in the information box.

  11. Untar charmm-gui.tgz and one can find the files of the cooridnate("step5_assembly.pdb") and topology("step5_assembly.psf"). These files will be further converted to the LAMMPS compatible input file.

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Nagoya University