One of the principal tools in the theoretical study of biological molecules is the method of molecular dynamics simulations (MD). This computational method calculates the time dependent behavior of a molecular system. These methods are now routinely used to investigate the structure, dynamics and thermodynamics of a lot of molecules. MD simulations generate information at the microscopic level, including atomic positions and velocities. In this thesis, MD is used for the simulations of two Amino acid ionic liquids systems. A refined force filed based on the AMBER force field reported by Zhou et al. [Zhou, G., Liu, X., Yu, G., He, H, J. Phys. Chem . 111 (2007) 7078-7084] was set up for two [P(C 4 ) 4 ][AA] ILs composed of tetrabutylphosphonium, [P(C 4 ) 4 ] + , cation with glutamine, [Gln] - , and leucine, [Leu] - , as the amino acid anions. The MD simulations were performed with the DL_POLY program (version 2.18) using a time step of 1.0 fs and R cutoff = 15.5 ?. The NPT Hoover ensemble was used for P = 1 atm and 321.85 K to calculate the structural properties and NVE ensemble was used to calculate the traort properties of these two systems. As an important check for the accuracy of simulation recipe is the comparison of experimental density with the density as obtained from simulation. The role of anion structure on the structural properties of [TBP][AA], have been investigated by looking at the radial distribution function(RDF) plots. For structural studying of cation, the dihedral angles of butyl chains in tetrabutyl phosphonium are calculated and the graph of dihedral angles distribution for all of the cations in simulation cell is drawn in the rang of 0 ° until 360 ° using a Fortran program. And finally, we have studied the mean square displacement (MSD) and diffusion coefficient (D) and comparred them with some similar Amino acid ionic liquids.
