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tractable only if the bulk of the remaining molecule is treated at a lower level of
theory[118].
In the present work we focus on the dynamics of proteins. A protein is a linear chain of
amino acid residues of 20 different types, the sequence of which (along with the solvent
environment, chaperones, cofactors, and binding partners) determines the final folded
conformation. They are particularly challenging systems because they are only
marginally stable.[1] Many methods have been developed to compute atomic motions in
proteins; the most accurate employ a force field which relates atomic positions, bond
lengths, bond angles, and dihedrals to potential. These force fields usually contain the
following:
E pot = " Vstretch + " Vangle + " Vtorsion + " VVanderWaals + " Velectrostatic Where the first two terms are typically modeled using quadratic potentials, and the third
with a harmonic potential. The Van der Waals interactions may be modeled using the
Lennard-Jones potential or others, while the electrostatic interactions are taken to act
between pointlike particles at the nuclear positions, having effective charges that largely
reflect the electronic charge distribution. The hydrogen bonding interactions are
absorbed into the electrostatic term by adjustment of the partial charges. The parameters
are obtained either through ab initio methods that compute the electronic wave functions
of molecules or, more often, by fitting to empirical data.
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