Replication Data for "Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models"

This dataset contains data for reproducing simulations described in Coppa et al., J. Chem. Inf. Model. 2023, 63, 10, 3030–3042; the "input" tree contains Amber input files for each simulation; the "starting_conformations" tree contains starting coordinates of each system in PDB format; the "traj" tree contains aMD trajectories (1500 ns), corresponding topology files, and amd.log files with weights. Trajectory files are in compressed .tar.bz2 format. Each tar archive, named as SYSTEM_FORCEFIELD_WATER.tar.bz2, contains a topology file (.prmtop amber7 format), two trajectory files (.nc netcdf format), one for the "extended" and one for the "misfolded" starting geometry, and the two corresponding aMD log files (plain text format). Trajectories and topologies have been stripped, leaving only the 100 waters that are the closest to the solute in each frame.