Simulations of POPC membranes of various shapes
Authors/Creators
- 1. Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
Description
Simulations of POPC membranes in 1) budded shape with Gaussian curvature and 2) wave shape with mean curvature but no Gaussian curvature and with two wavelengths ("long" and "short"), and 3) a freely fluctuating membrane.
Simulations were performed using GROMACS simulation engine (DOI: 10.1016/j.softx.2015.06.001 ) and the Martini 2 force field ( DOI:10.1021/jp071097f ). The budded and wavy geometries generated using BUMPy ( DOI: 10.1021/acs.jctc.8b00765 ) are maintained using restrained dummy particles that repel lipid acyl chains
All input and output files are provided for each simulation, and the cpt files allow to extend the simulations. Additionally, topologies (in the TOP.tar archive) and simulation parameters (md.mdp) are provided.
Some of the simulations have been used in DOI: 10.1101/2020.09.23.310086 and DOI: 10.26434/chemrxiv-2021-6wksn
Files
Files
(17.6 GB)
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