Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.

ABSTRACT: In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would b

SUBMITTER: Marcisz M 

PROVIDER: S-EPMC10091405 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature