This folder contains input files for a simulation of a tiny system (27 atoms) composed by one tetramethylammonium molecule and one acetone molecule.

Files necessary to run the system with NAMD (force field, PSF/PDB, etc) are in the Common folder.

Other folders contain inputs to run the most common biasing & sampling methods implemented by Colvars:

• smd: Steered Molecular Dynamics, with integration of the work performed on the restraint center
• us: umbrella sampling (WHAM inputs are not included)
• abf: Adaptive Biasing Force (ABF), using the total-forces estimator (classic thermodynamic integration)
• mtd: metadynamics

ABF is directly based on thermodynamic integration (TI), but it is also possible to use the TI free energy estimator for other biases: add the keyword writeTIPMF yes to the configuration of the harmonic or metadynamics biases.