Lipid membrane simulations with flat-bottom and double-bilayer setups, part 2/2
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2023-06-08, 2023-06-08
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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 only double-bilayer simulations. The flat-bottom simulations together with all topologies and mdp files can be found in part 1 : DOI: 10.5281/zenodo.7973838
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