Lipid membrane simulations with flat-bottom and double-bilayer setups, part 1/2

To cite: Biriukov, D. and Javanainen, M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J. Chem. Theory Comput. 2023, 19 (18), 6332–6341. DOI: 10.1021/acs.jctc.3c00614

Gromacs molecular dynamics simulations to compare membrane and solvent properties from lipid membrane simulations with flat-bottom and double-bilayer setups. CHARMM36 force field was used except for simulations with peptides, where a prosECCo model was used [Nencini et al., Biophys. J. 121, 157a (2022)]

This dataset contains all the topologies and flat-bottom simulation files. The double-bilayer simulation files can be found in part 2: DOI: 10.5281/zenodo.7974633

Abbreviations in the names of simulation files:

"fb" - simulations with a flat-bottom setup

"2m" - simulations with two lipid membranes, i.e., a double-bilayer setup

"popc" - membrane is modeled as a POPC lipid bilayer

"mix" - a realistic membrane with various lipids is modeled, resembling the composition from [Lorent et al., Nat. Methods 16, 644–652 (2020)]

"nak" - only sodium and potassium cations, together with chloride anions, are present in the system

"ext" - as "nak", but also calcium and magnesium cations are added

"r9" - as "nak" but also R9 (nona-arginine) peptides are added on both sides of the membrane

"r9k" - as "nak" but also R9 (nona-arginine) peptides are added on the extracellular side of the membrane

"one" - ions are present only on one side of a lipid membrane

"freecl" - flat-bottom simulations but without restraints on chloride anions

"s" - simulations were performed using the scaled-charge prosECCo75 force field based on CHARMM [Nencini et al., Biophys. J. 121, 157a (2022)]

"restr" - restraint .gro file with ionic/peptide z coordinates set to zero