The purpose of this document is to instruct the user in simulating ionic liquids at room temperature and calculating Radial Distribution Functions (RDFs) through the use of Amber, AmberTools and VMD.

Room-temperature ionic liquids are, as the name suggests, salts that exist in liquid states at room temperature. RTILs are of great interest to a variety of fields because they exhibit unique physical and thermodynamic properties, such as negligble vapor pressure, high thermal stability, high electrochemical stability, and low flammability. Moreover, ionic liquids exhibit high conductivity and a wide electrochemical window, which means that they are neither easily oxidized nor reduced, hence they are excellent candidates for efficient and green electrolytes in batteries. Due to the various potential applications RTILs promise, computer simulations of RTILs have widely propagated, and various combinations of different cations and anions have been designed and tested to further increase our knowledge in this field.

In this tutorial, we will be generating an ionic liquid mixture of 1-Butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) and Acetonitrile (CH3CN) to replicate the data in the paper: X. Wu, Z. Liu, S. Huang and W. Wang, “Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF4] and acetonitrile by a refined force field”,  Phys. Chem. Chem. Phys  7, 2771-2779 (2005). See also Z. Liu, S. Huang and W. Wang, “A refined force field for molecular simulation of imidazolium-based ionic liquids”,  J. Phys. Chem. B  108, 12978-12989 (2004).

Please note: this tutorial uses the general Amber force field (GAFF) force field to create an initial (not a “refined”) force field. Some aspects of the simulation results are not in as good agreement with experiment as the results presented in the papers listed above. This is a good object lesson: GAFF can get you started, and can provide results of reasonable accuracy. Depending on your needs, this may be enough. But it is often desirable to treat the GAFF results as a starting point for further refinement; the latter is usually system-specific, and is not covered in this tutorial.