A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization
Jazyk angličtina Země Spojené státy americké Médium print
Typ dokumentu časopisecké články, přehledy
PubMed
32770904
DOI
10.1063/5.0017775
Knihovny.cz E-zdroje
- MeSH
- DNA chemie MeSH
- lidé MeSH
- membránové lipidy chemie MeSH
- proteiny chemie MeSH
- RNA chemie MeSH
- simulace molekulární dynamiky * MeSH
- statická elektřina MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- DNA MeSH
- membránové lipidy MeSH
- proteiny MeSH
- RNA MeSH
Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.
Citace poskytuje Crossref.org
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?
Building Water Models Compatible with Charge Scaling Molecular Dynamics
Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers
Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin
Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension