Optimal Recovering of the Folding/Unfolding Equilibrium of a Model Peptide Via Replica Exchange Simulations Using GROMACS/PLUMED

Folding/UnfoldingEquilibrium of a Model Peptide Via Replica ExchangeSimulations Using GROMACS" by Michele Casoria et al. Data are from REM simulations done with GROMACS 2022.3 patched with PLUMED_2.8.4 Directory tree .├── bin scripts for computing flux and demuxed rmds sd and average; │ the scripts panel_*.py produce REM analysis data for Figure 5 of ms.pdf ├── ST1 ├── F │ └── U├── ST2│ ├── F│ └── U├── ST-w│ ├── F│ └── U└── T-REM ├── F ├── U └── U_cubo├── pdf (main paper) ├── pdb (Chignolin reference structures) In each U/F directory for the four protocols ST1, ST2, ST-w, T-REM the following data are reported:- md.log (replica 1)- replica_*.xvg- rmsd*hst (reference structure beta-turn 1UAO ) : RMSD histograms for walkers and nodes- demux_rmsd*.xvg: RMSDs of demultiplexed trajectories- rmsd_298.xvg ( target state RMSD time record) - traj1.pdb (target state trajectory; peptide only)