Calculations of interactions in biomolecular systems: comparison of quantum and classical approaches

Methodical aspects of molecular mechanics, quantum chemistry, and combined quantum mechanics/molecular mechanics (QM/MM) approaches are discussed with respect to the intermolecular interaction calculations between some aminoacids (arginine, histidine, and serine) and water molecules. Calculations are implemented on the supercomputer SKIF-MGU “Chebyshev” by using the density functional theory to describe quantum subsystems. Some practical recommendations are formulated on the basis of numerical results.