Molecular dynamics (MD) has been used to simulate the liquid chromatography process. The flow speed was arbitrarily increased to save computer time. Then the average translational motion is still relatively slow and does not perturb the interaction of the solute with the stationary phase. The CHFClBr molecule was used as model chiral system, with water as a solvent. The MD technique with a standard potential provided realistic all-atomic simulations of the separation ratios and enabled to test the sensitivity of the process to solvent polarity and temperature. Low temperature and non-polar solvent favored the separation.