Ontology highlight
ABSTRACT:
SUBMITTER: Olsson MA
PROVIDER: S-EPMC5074236 | biostudies-other | 2016 Jun
REPOSITORIES: biostudies-other
Olsson Martin A MA Söderhjelm Pär P Ryde Ulf U
Journal of computational chemistry 20160427 17
In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltz ...[more]