Embedding Nonrigid Solutes in an Averaged Environment: A Case Study on Rhodopsins.

ABSTRACT: Many simulation methods concerning solvated molecules are based on the assumption that the solvated species and the solvent can be characterized by some representative structures of the solute and some embedding potential corresponding to this structure. While the averaging of the solvent configurations to obtain an embedding potential has been studied in great detail, this hinges on a single solute structure representation. This assumption is re-examined and generalized for conformationally flexible solutes and tested on 4 nonrigid systems. In this generalized approach, the solute is characterized by a set of representative structures and the corresponding embedding potentials. The representative structures are identified by means of subdividing the statistical ensemble, which in this wor

SUBMITTER: Ricardi N 

PROVIDER: S-EPMC10413860 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature