On calculating the bending modulus of lipid bilayer membranes from buckling simulations
Authors/Creators
- 1. 1. University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France , 2. Bioactive Molecules Research Laboratory, Doctoral School of Sciences and Technologies, Faculty of Sciences, Lebanese University, Lebanon
- 2. 1. University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France, 2. Laboratory of Computational Quantum Chemistry and Drug Design, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
- 3. Bioactive Molecules Research Laboratory, Doctoral School of Sciences and Technologies, Faculty of Sciences, Lebanese University, Lebanon
- 4. Laboratory of Computational Quantum Chemistry and Drug Design, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
- 5. University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France
Description
Molecular dynamics simulations files that correspond to the buckling simulations method to calculate the bending modulus and the box area fluctuations method to calculate the area compressibility modulus. We performed all molecular dynamics (MD) simulations using the GROMACS software (v. 2016.4) and the MARTINI coarse-grained (CG) force field (v. 2.2), using standard simulation parameters. Each file contains GRO, TOP, ITPs, and MDP files that correspond to the equilibration and the production runs. The name of each folder indicates the types of lipids. We simulate single-component lipid bilayers includes: DLPC, (14:0-14:0), DPPC (16:0-16:0), POPC (16:0-18:1), DOPC (18:1-18:1), PUPC (16:0-22:6), DLiPC (18:2-18:2), DNPC (24:6-24:6), POPG (16:0-18:1), POPS (16:0-18:1), POPE (16:0-18:1), and DPSM (16:0-16:0), and lipid mixtures includes : DOPC:CHOL, DPPC:CHOL, POPC:POPE, DPPC:DLPC, POPC:PUPC, DNPC:DLPC, and DPPC:DLiPC:CHOL, with different molar ratios specified in the folders names.