#OpenMM Python scripts

These folders contain various Python scripts to setup and run simulations using OpenMM. Since some options are forcefield-specific, the scripts are divided accordingly.

AMBER FF

The scripts under the amberff folder are to be used with the AMBER family of forcefields. By default, the scripts use amberff14sb and tip3p as the water model. Lipids use the lipid17 parameter set.

Each of the scripts performs a specific task in the simulation setup and should be used roughly in the following order:

• buildSystem.py: adds hydrogens and ensures atom/residue names are valid according to the forcefield naming rules.
• setPeriodicBox.py: calculates the box vectors to create a periodic box that encloses the system.
• minimizeSystem.py: performs restrained (heavy atoms only) energy minimization. To perform an unrestrained EM, just set to force constant to 0.
• solvateBox.py/addMembrane.py: add solvent (water), counter-ions, and a membrane bilayer to the system. Use one or the other.
• heatSystem.py: introduces velocities to the system by slowly increasing temperature up to a desired value. You can control how slow/gradual this increase is.
• equilibrate_NxT.py: run restrained (by default) MD on a system, with/without pressure coupling.
• runProduction.py: runs unrestrained production MD.

You should prepare your system using the scripts in the utils folder, and then feed a mmCIF to buildSystem.py to start your simulation setup.

Known issues:

• Cubic boxes only. Triclinic simulation boxes give weird issues.