Molecular Dynamics Simulations in Statistical Physics: Theory and Applications by Hiqmet Kamberaj

Author:Hiqmet Kamberaj
Language: eng
Format: epub, pdf
ISBN: 9783030357023
Publisher: Springer International Publishing

7.2 Features of Molecular Mechanics Force Fields

A molecular mechanics force field is defined not only by the functional form, but also the parameters (such as k i,l, k i,θ, V n, ε ij, σ ij, and q i) in Eq. 7.1. An essential feature is that two force fields may have the same functional form, but at the same time very different set of parameters. Moreover, different force fields may give approximately the same accuracy in calculations. Furthermore, different force fields cannot be mixed; that is, it is not strictly allowed to divide the energy into individual terms, and take some of the parameters from one force field and mix them with parameters from another force field. However, some of the terms in a molecular mechanics force field are sufficiently independent of the others (e.g., bond stretching and angle bending terms) to make this approximation acceptable in some cases.

The non-bonded interactions determine the thermodynamic equilibrium and processes, such as folding/unfolding, membrane, and micelle formation, ligand-, DNA- and protein-protein binding, solvation (in membrane and water). Therefore, there exist three main problems in the parametrization of a mechanical force field (van Gunsteren et al. 2006): minimal free energy differences and many interactions, entropic effects, and variety of atoms and molecules.

It worth noting that molecular mechanics force fields are empirical; that is there is no correct form for a force field. In principle, if one potential energy functional form performs better than another force field, then it is likely that force field will be favored. There have been many efforts to compare the accuracy of different force fields. The potential energy functional form used in a force field is a compromise between accuracy and computational efficiency. Thus, we expect with increasing the computer performance, more complex functional forms will be possible to incorporate into molecular mechanics force fields. Besides this, the new potential functional forms should allow fast calculations of the first and second order derivatives of energy function with respect to atomic coordinates to use methods such as energy minimization and molecular dynamics.

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