The ELBA-LAMMPS toolkit is a collection of tools aimed at facilitating the simulation of the ELBA model in LAMMPS. More concretely, ELBA-LAMMPS can be described as a LAMMPS add-on package providing users with various functionalities to setup, run and analyze molecular dynamics simulations of systems modeled with the ELBA force field.
The ELBA model is described in the following papers:
- Stress testing the ELBA water model, W. Ding, M. Palaiokostas, and M. Orsi, Mol. Simul. 42, 1 (2016).
- Comparative assessment of the ELBA coarse-grained model for water, M. Orsi, Mol. Phys. 112, 1 (2014).
- Direct Mixing of Atomistic Solutes and Coarse-Grained Water, M. Orsi, W. Ding, and M. Palaiokostas, J. Chem. Theory Comput. 10, 4684 (2014).
- Physical properties of mixed bilayers containing lamellar and nonlamellar lipids: insights from coarse-grain molecular dynamics simulations, M. Orsi and J. W. Essex, Faraday Discuss. 161, 249 (2013).
- The ELBA force field for coarse-grain modeling of lipid membranes, M. Orsi and J. W. Essex, PLoS One 6, e28637 (2011).
The various folders in the ELBA-LAMMPS toolkit contain usage information in the form of README files.
examples: various test runs, which can be used to check the LAMMPS build, to understand how to run and analyze ELBA systems, and as starting points for new simulations
tools: scripts performing various operations, such as analysis of LAMMPS output files to extract properties of interest and file manipulation to enable trajectory visualization; check comments at the top of each file to find usage information
viz: status files for visualization of ELBA systems with VMD