Constant pH MD Simulation data for AL55 VL domain

This dataset contains the input and output files from constant-pH molecular dynamics (CpHMD) simulations of the AL55 VL domain performed at pH 4.0 and pH 6.5. For each pH condition, three independent replicates (R1, R2, R3) were simulated using gromacs software. Each system folder includes: MD.tpr MD_dt100ps.xtc: Trajectory file with coordinates saved every 100ps MD.mdp: MDP file generated using CpHMD Gromacs code and used for simulation. index files: Index groups defining λ-states lambdareference.dat: Details on which residues were treated as titratable.