LocalSCF
 | Understanding the mechanisms of macromolecular systems builds on appreciation of reach physics of the underlying atomistic processes. It is well understood, that atomistic processes are governed by quantum-mechanical (QM) principles. This includes the effects of intermolecular charge transfer and polarization, bond breaking and formation, accounting for processes happening at hydrophobic-hydrophilic interfaces and for temperature dependence of physical properties of the materials. To keep the low computational overhead it is necessary to use certain approximations to the QM scheme. LocalSCF is one of such methods utilizing local properties of molecular systems. Due to its modest computational requirement LocalSCF opens the possibility to study thermodynamic properties of liquids and solids, drug-receptor interactions, enzyme catalysis, free energies, and provides insights into many processes which require rigorous sampling of the potential energy surface by employing molecular dynamics. |
Ubiquitin in water droplet; 12199 atoms; 20 ps QM MD
Validation of 2-layer all-atom QM Method for Protein-Ligand Docking  | Difference in Total Energy as a function of buffer-zone thickness 2-layer QM / QM method converges to the conventional 1-layer QM on buffer-zone thickness from 6 to 12 Å. Buffer zone is part of the protein located in close proximity to the bound ligand. Buffer zone and ligand are treated at regular SCF level while the protein bulk density matrix is frozen. The character of energy convergence suggests that treating only the ligand at QM level while considering the protein at MM level will not be equivalent to the full-QM picture in capturing the effects of electrostatic polarization. |
Anisimov V.M., Bugaenko V.L., J. Comput. Chem., 2009, 30 (5) 784. |