This example shows how to put a protein (inclusion) in a
lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
The DPPC lipid model is described here:
G. Brannigan, P.F. Philips, and F.L.H. Brown,
Physical Review E, Vol 72, 011915 (2005)
(The new DLPC model is a truncated version of DPPC.)
The protein model is described here:
G. Bellesia, AI Jewett, and J-E Shea,
Protein Science, Vol19 141-154 (2010)

Note:
This example may require additional features to be added to LAMMPS.
If LAMMPS complains about an "Invalid pair_style", then copy the code
in the "additional_lammps_code" directory into your LAMMPS "src" directory
and recompile LAMMPS.

----- Details --------

This example contains a coarse-grained model of a 4-helix bundle protein
inserted into a lipid bilayer (made from a mixture of DPPC and DLPC).

-- Protein Model: --

The coarse-grained protein is described in:
G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
Here we use the "AUF2" model described in that paper.
(The hydrophobic beads face outwards.)

-- Memebrane Model: --

The DPPC lipid bilayer described in:
G. Brannigan, P.F. Philips, and F.L.H. Brown,
Physical Review E, Vol 72, 011915 (2005)
and:
M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
J. Chem. Phys. 135, 244701 (2011)

As in Watson(JCP 2011), rigid bond-length constraints
have been replaced by harmonic bonds.

A truncated version of this lipid (named "DLPC") has also been added.
Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
parameterized to reproduce the correct behavior in a lipid bilayer mixture.



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Instructions on how to build LAMMPS input files and
run a short simulation are provided in other README files.

step 1)
README_setup.sh

step2)
README_run.sh