Data for: "Martinoid: The Martini Peptoid Force Field"

The contents of the folders are outlined below, for specific information pertaining to a given files relevance please refer to the README.txt file within each sub-directory. The folders are grouped in terms of thier usage within parameterisation process: Bonded Term Mapping: ~~~~~~~~~~~~~~~~~~~~ > Additional Residues - MP2/6-31G(d) torsion scans and atomistic term fitting files for residues NmO, Ns and Nt as well as files for partial charge fitting following the method outlined in the article available at (https://doi.org/10.1021/acs.jpcb.3c03725). > BackboneMapping - all atom (AA) and coarse grained (CG) trajectories and tools for comparison of BB-BB-BB angle term choice at the CG level. > MappingTrajectories - all atom (AA) and coarse grained (CG) trajectories and tools for comparison of BB-BB-BB angle term choice at the CG level for a variety of peptoid trimers. > HelicalOptimisation - all atom (AA) and coarse grained (CG) trajectories and tools for comparison of BB-BB-BB angle and BB-BB-BB-BB dihedral term choice at the CG level for (Nk-Nfes-Nfes)2 helical fragment. > SWARMCGOptimisedITPS - optimised *itp structure files for peptoid dimers as identified by SWARMCG and with which the superimposed parameter sets are generated. > FinalAssemblyAc-Nf-Nf - assessment of impact of parameter superposition for dimer Ac-Nf-Nf, trajectories and measurement tools. Nonbonded Term Mapping: ~~~~~~~~~~~~~~~~~~~~~~~ > AssemblyStudy - single monomer self-assembly study for peptoids to assess the accuracy of bead type selection for these species by assessing whether aggregation occurs/does not occur. > CG_LogD - relevant files for estimating the LogD of various peptoid monomers to assess whether bead choices were sufficently accurate. > HPLC_LogD_Data - chromatograms for peptoid monomers onbtained experimentally using a gradient of H2O : acetonitrile (+ 0.1 % TFA). > NMRCharacterisation - structural validation of pure peptoid monomer material. Model Validation Data: ~~~~~~~~~~~~~~~~~~~~~~ > TrimerAssembly - assembly of Nf-Nke-Nf in form of tape across PBC, this is relevant for comparison to experimnetal Cryo-TEM measurements. > FreeAssemblyNf-Nke-Nf - experimnet to illsutrate 2D bilayer like structures are formed by this trimer, forming the basis for the TrimerAssembly preposition that the nanostriations seen experimnetally are 'tape-like' > NanosheetStudy - validation of parameterisation method using peptoid nanosheet forming oligomers at oil-water interface, validating within a reasonable margin the length of said oligomers in the assembled state. Hamish W. A. Swanson (04.12.23)