When using any file from this archive, please cite:

J. Karl Spinti, Fernando Neiva Nunes and Manuel N. Melo
Room for Improvement in the Initial Martini 3 Parameterization of Peptide
Interactions, 2022

This archive contains a tree with starting configurations, GROMACS peptide
topology files and GROMACS run input files that can be used in recreating the
simulations as in the paper. Additional topology files not developed in this
study are needed -- such as lipid, solvent and ion topologies. These, together
with the main Martini2 and 3 particle definition files can be obtained from
http://cgmartini.nl

Alongside the files needed for system simulation are include the result files
from the peptide contact and helix tilt analyses described in the paper. The
data is presented in NumPy format (.npy extension), and is readable using the
same library. Results from umbrella-sampling PMF calculation are presented in
tabular text frmat (files fes.xvg).
