Protein dynamics via computational microscope

Figure 1 An example of the equation used to calculate atomic forces. The equation describes potential energy in the Assisted Model Building with Energy Refinement force field. The first summation term represents the energy between the covalently bonded atoms. Summing of the angles, second term, represents the energy due to the angle geometry. Third term represents the energy of the torsion angles. Forth term accounts for the energy of the non-bonded interactions between all pairs of atom. This term can be decomposed into van der Waals and electrostatic energies. The subscript zero represents equilibrium values. The energy terms are parameterized to fit experimental (for example, spectroscopic) data and/or quantum-mechanical calculations.