Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields.

ABSTRACT: Dimerization free energies are fundamental quantities that describe the strength of interaction of different molecules. Obtaining accurate experimental values for small molecules and disentangling the conformations that contribute most to the binding can be extremely difficult, due to the size of the systems and the small energy differences. In many cases, one has to resort to computational methods to calculate such properties. In this work, we used molecular dynamics simulations in conjunction with metadynamics to calculate the free energy of dimerization of small aromatic rings, and compared three models from popular online servers for atomistic force fields, namely G54a7, CHARMM36 and OPLS. We show that, regardless of the force field, the profiles for the dimerization free energy of the

SUBMITTER: Patmanidis I 

PROVIDER: S-EPMC8512883 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature