Molecular dynamics simulation data for Ala5.
The peptide was simulated using the Amber99-sbildn forcefield, GBSA implicit solvent, and Langevin dynamics at 300 K with 50/ps damping. Positions were written every 10 ps. The PDB file was prepared with PDBFixer, and the simulation was performed with OpenMM.
The model is located under model, while the run_ala5_sim.sh and amber_gbsa.py scripts were used to run the simulation. The data itself is located under simulation_data.
You will need to install the Git Large File Storage plugin to clone the repo.