C++ script which generates a LAMMPS script membrane_finite.in and data file membrane_finite.dat. Parameters are read in from params_membrane_finite.txt.
Variable parameters for simulation. Each parameter is the only entry on a line. For the order and description of parameters, see the commented parameter input section of membrane_finite.cpp.
LAMMPS script modeling a bilipid membrane in a periodic simulation box filled with DPD fluid. membrane_finite.dat must be in the same directory to run. This script runs with the version of LAMMPS compiled Aug. 10, 2015.
Outputs:
membrane_finite.lammpstrj- LAMMPS trajectory file for visualization. Loadable in, e.g., VMD. Does not include fluid
Data file which stores the initial positions of the lipids in a bilayer membrane. Includes positions, bonds, and angles.
Matlab script for image analysis. Reads bitmap files rendered by VMD's frame export. Used for computing radius of pores (front view) and membrane widths (side view).