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LAMMPS-PoratedMembrane

membrane_finite.cpp

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.

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.

membrane_finite.in

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

membrane_finite.dat

Data file which stores the initial positions of the lipids in a bilayer membrane. Includes positions, bonds, and angles.

vmd_analysis.m

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).