title: mRNA lipid nanoparticle phase transition
author: Trollmann, Marius F.W.
description: The repository contains input files and data from the manuscript: Trollmann, Marius F.W. and Böckmann, Rainer A. "mRNA lipid nanoparticle phase transition", Biophysical Journal (2022) https://doi.org/10.1016/j.bpj.2022.08.037   > Periodic membrane patches Equilibrated structures, .mdp and .top files for the simulations of the periodic Comirnaty membrane patches. (microsecond = us) >> periodic_patches/low_ph/single_patch:  ~ System A: Three replicas (4.1 us, 3.0 us and 3.0 us) of the self-assembled Comirnaty lipid mixture with the protonated aminolipid >> periodic_patches/low_ph/quad_patch:  System B: A quadruplicated system A patch simulated for 1.0 us >> periodic_patches/dspc_chol: System C: Binary membrane including DSPC and 43mol% cholesterol >> periodic_patches/neutral_ph: System D: A deprotonated system B patch simulated for 0.633 us >> periodic_patches/mrna_selfassembly: System E: Structures of the self-assembled Comirnaty lipid mixture with the modified mRNA strand + periodic_patches/mrna_selfassembly/selfassembly: Structures of the mRNA-lipid mixture after self-assembly with protonated aminolipids + periodic_patches/mrna_selfassembly/set1: Quadruplicated simulation systems after deprotonation of distant aminolipids (set 1, see paper)  + periodic_patches/mrna_selfassembly/set2: Quadruplicated simulation systems after deprotonation of random aminolipids (set 2, see paper) + periodic_patches/mrna_selfassembly/set3: Simulation systems after deprotonated of all aminolipids (systems were not quadruplicated) (set 3, see paper)   > Lipid nanoparticles Equilibrated structures, .mdp and .top files for the simulations of the lipid nanoparticles. (microsecond = us) >> nanoparticles/lnp_nopegs: System F: Structures of the lipid nanoparticles with capped PEGylated lipids >> nanoparticles/lnp_pegs: System G: Structure of the lipid nanoparticle with complete PEGylated lipids              > Topologies - topology/DSPC.top - Parameters for the standard phospholipid from the CHARMM36 forcefield - topology/CHOL.top - Parameters for cholesterol from the CHARMM36 forcefield - topology/alc.itp, topology/alc.prm - Parametrization files of the PEG-ylated lipid ALC-0159 obtained from the CGenFF-Webserver - topology/alc_neutral.itp - Parameters for the neutral aminolipid ALC-0315 obtained from the CGenFF-Webserver - topology/alc_protonated.itp - Parameters for the protonated aminolipid ALC-0315 obtained from the CGenFF-Webserver - topology/modRNA.top - Parameters for the short modified mRNA strand. Uridine was replaced with N1-Methylpseudouridine. The parameters were not included in the standard CHARMM36 forcefield (version July 2020) and were manually added to the forcefield. - topology/ALC_SHORT_CORRECT_IDX.itp - Parameters for the capped PEG-ylated lipid ALC-0159 -> Parameters were manually adapted to fit the shortened structure. - topology/charmm36-jul2020.ff - CHARMM36 forcefield parameters (version July 2020) with included parameters for N1-Methylpseudouridine. - topology/cgenff_output - Output from the CGenFF-Webserver to parametrize the aminolipid (ALC-0315) and the PEGylated-lipid (ALC-0159)    