## 2 Materials and Methods
### Methods
#### 2.2.7 Molecular Dynamics Simulations  
The receptor-ligand MD studies were conducted using Desmond in Schrodinger Suites version 2021-4 and the OPLS4 force field for 100 ns with each of the receptor-ligand complexes [60; 61; 62; 63]. The output receptor-ligand structures from AutoDock Vina were used as MD inputs. Maestro's Protein Preparation Wizard was used to prepare the PHF tau (PDB ID: 503L) receptor structure by assigning bond orders with the CCD database, creating disulfide bonds, adding hydrogens and generating ionization states using Epik at pH 7.4 [64]. The system builder option on Maestro was used to define the simulation box boundary along with the buffer distance between the solute structures and the box. For this simulation, an orthorhombic box was used with distances (side lengths) of 10 A away from the receptor-ligand structure along on all sides. For solvation, SPC water molecules were used, and the system was neutralized through the addition of either Na\({}^{+}\) or Cl\({}^{-}\) counter ions. The system was set up with a 0.15 M NaCl concentration. Each simulation began with Brownian Dynamics in the NVT ensemble (T = 10 K) withrestraints on solute heavy atoms and small time steps of 100 ps. Next, NVT equilibration was run (T = 10 K) with restraints on solute heavy atoms and small time steps for 12 ps. Next, NPT equilibration was run (T = 10 K) with restraints on solute heavy atoms for 12 ps, followed by NPT equilibration (T = 300 K) with restraints on solute heavy atoms for another 12 ps. Finally, NPT equilibration was run (T = 300 K) with no restraints for 24 ps. The production MD was run in the NPT ensemble (T = 300 K) for 100 ns with a time step of 2 fs. We first simulated the system in NVT ensemble with Brownian dynamics at 10 K with solute heavy atoms restrained to ensure that the system does not become unstable. Furthermore, low temperatures facilitate constraining of the atoms in small time steps. Fixed volume was utilized to avoid abrupt changes in the volume due to strong attractive or repulsive forces. The initial NVT runs with backbone atoms constrained thus allowed side chain atoms to begin slow movement. After the system was equilibrated at a low temperature, we increased the temperature to the desired temperature (300 K) and used the preferred ensemble with no restraints [65]. This method also allows for initial minimizations to remove undesired contacts between solvating water molecules introduced into box. The Maestro simulation interactions diagram was used to summarize the stabilities and interactions of the structures for each simulation. Upon completion of the receptor-ligand MD studies, the Desmond Trajectory Frame clustering option on Maestro was utilized to perform clustering calculations on structures based on the RMSD matrix of trajectory files. The trajectory and frames for each run were specified via the -out.cms file that had been generated from the receptor-ligand MD studies. The RMSD of the backbone for the clustering was set to calculate at every tenth frame after 75 ns. Using the RMSD matrix, the affinity propagation clustering method [66] was then used to cluster the frames. Once the clustering job was completed, it generated a.cms file with a frame from each cluster as well as a log file containing the total number of clusters as well as their sizes.