DOI: 10.5281/zenodo.12805208
title: MD data for Ionizable cationic lipids and helper lipids synergistically contribute to RNA packing and protection in lipid-based nanomaterials

description: 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