Files associated with the manuscript entitled: Assessment of the MARTINI 3 Performance for Short Peptides Self-assembly
Folders content:
- analyses/ analysis scripts required to carry out the analysis described in the manuscript:
- gradients analysis as described by Thallmair et al (DOI: 10.1021/acs.jpcb.1c03665)
- radial distribution function (RDF) of the backbones and of the side chains
- solvent accessible surface area (SASA), required to calculate the aggregation propensities (AP). AP=SASA0/SASAf. SASA0=initial SASA; SASAf=final SASA
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peptides_itp/ itp and pdb files of all the peptides studied with the different models.
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simulations_mdps/ mdp files with all the simulation parameters employed. Standard is the one used unless otherwise specified.
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structures/ gro files of the final structures presented in the manuscript.