A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F20%3A00531628" target="_blank" >RIV/61388963:_____/20:00531628 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1063/5.0017775" target="_blank" >https://doi.org/10.1063/5.0017775</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1063/5.0017775" target="_blank" >10.1063/5.0017775</a>

Jazyk výsledku

angličtina

Název v původním jazyce

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2020

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Chemical Physics

ISSN

0021-9606

e-ISSN

—

Svazek periodika

153

Číslo periodika v rámci svazku

5

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

15

Strana od-do

050901

Kód UT WoS článku

000559816300001

EID výsledku v databázi Scopus

2-s2.0-85089261949