All simulations of MUP1 start from a protein-ligand complex with PDB code 1I06. The crystal ligand was removed but crystallographic waters were retained. The protein was protonated according to a pH of 7.0 using PDBFixer. Missing loops were added where appropriate with PDBFixer and the protein termini were capped using N-methyl and acetyl caps. The system was then solvated in a box of TIP3P water with a buffer of 12 Å around the protein. NaCl ions were added to neutralize the system and further added to a concentration of 0.15 M.