MD data for Ionizable cationic lipids and helper lipids synergistically contribute to RNA packing and protection in lipid-based nanomaterials

The data stored in this repository is part of the journal article: Zimmer, D. N., Schmid, F., & Settanni, G. (2024). Ionizable Cationic Lipids and Helper Lipids Synergistically Contribute to RNA Packing and Protection in Lipid-Based Nanomaterials. The Journal of Physical Chemistry B https://doi.org/10.1021/acs.jpcb.4c05057 Data of multiscale simulations of DLinDMA:DOPE:Cholesterol, DLinDMA:DSPC:Cholesterol, DLinDAP:DOPE:Cholesterol and DLinDAP:DSPC:Cholesterol in the presence of RNA. For each formulation, data is provided with different coarse-grained parameterizations (generic, adapted) and differents treatments of the RNA (ELN, noELN). Provided are the first and the final frame of each run, the associated topologies, and the respective gromacs input files. > M_PE, M_PC, P_PE, P_PC DLinDMA:DOPE:Cholesterol, DLinDMA:DSPC:Cholesterol, DLinDAP:DOPE:Cholesterol and DLinDAP:DSPC:Cholesterol in presence of a 40mer RNA fragment. cg_generic+aa: cg: 2 microsecond production run based on a generic MARTINI parametrization md_0.gro: first frame md_10.gro: final frame cg_rna_bilayer.top: Topology of the system cg_DLD{M/P}_lipid.itp: generic MARTINI topology of DLinDMA/DLinDAP martini_v2.0_CHOL_02.itp, martini_v2.0_DSPC_01.itp, martini_v2.0_ions, martini_v2.1.itp, martini_v2.1-dna.itp: Several MARTINI topology files for molecules not included in MARTINI Nucleic_A.itp or Nucleic_A_eln.itp: Topology of the RNA fragment for MARTINI aa: 300/600 nanosecond production run based on CHARMM36 md_0.gro: first frame md_60.gro: final frame backmapped.top: Topology of the system (including the parametrization of DLinDMA/DLinDAP) CHOL.itp, DOPE.itp, DSPC.itp, 40mer_autopsf.itp: topology files for Cholesterol, DOPE, DSPC and RNA fragment as they are not part of the standard molecules in CHARMM36. ELN and noELN indicate presence or absence of an elastic network to fix the structure of the RNA during the cg runs. cgmdp: Gromacs input files for the cg runs aamdp: Gromacs input files for the aa runs cg_adapted+aa: cg: starting and ending frame of a 2 microsecond production run based on an adapted MARTINI parametrization md_0.gro: first frame md_10.gro: final frame cg_rna_bilayer.top: Topology of the system martini_v2.0_DIDMA_20 or martini_v2.0_DIDAP_20: generic MARTINI topology of DLinDMA/DLinDAP martini_v2.0_CHOL_02.itp, martini_v2.0_DSPC_01.itp, martini_v2.0_ions, martini_v2.1-dna_cr1_POL_NACL.itp: Several MARTINI topology files for molecules not included in MARTINI Nucleic_A.itp or Nucleic_A_eln.itp: Topology of the RNA fragment for MARTINI aa: 300/600 nanosecond production run based on CHARMM36 md_0.gro: first frame md_60.gro: final frame backmapped.top: Topology of the system (including the parametrization of DLinDMA/DLinDAP) CHOL.itp, DOPE.itp, DSPC.itp, 40mer_autopsf.itp: topology files for Cholesterol, DOPE, DSPC and RNA fragment as they are not part of the standard molecules in CHARMM36. ELN and noELN indicate presence or absence of an elastic network to fix the structure of the RNA during the cg runs. cgmdp: Gromacs input files for the cg runs aamdp: Gromacs input files for the aa runs