Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F20%3A00519393" target="_blank" >RIV/61388963:_____/20:00519393 - isvavai.cz</a>

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00813" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.9b00813</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.9b00813" target="_blank" >10.1021/acs.jctc.9b00813</a>

Result language

angličtina

Original language name

Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections

Original language description

Overbinding of ions is a common and well-known problem in classical molecular dynamics simulations. One of its main causes is the absence of electronic polarizability in the force fields. The current approaches for minimizing overbinding typically either retain the original charges and use an ad hoc readjustment of the Lennard-Jones parameters as done in the nonbonded fix (NBFIX) approach or rescale the charges using a theoretical framework. The goal in the latter is to include shielding produced by the missing electronic polarizability as done in the electronic continuum correction (ECC) approach. NBFIX and ECC are the most common corrections, and we compare their performance to the default parameterizations provided by five different commonly used biomolecular force fields, OPLS-AA/L, CHARMM27, CHARMM36m, CHARMM22*, and AMBER99SB-ILDN. As test systems, we use poly-α,L-glutamic and poly-α,L-aspartic amino acid molecules in explicit water together with Na+ and K+ counterions. We demonstrate that the different force fields yield results that are not only quantitatively but also qualitatively different. The resulting structures of the macroions depend strongly on the model for ions. NBFIX corrections alleviate the problem of overbinding, resulting in extended peptides. The ECC corrections depend nontrivially on the original underlying model, and despite being based on a theoretical framework, they cannot always solve the problem.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

Project

<a href="/en/project/GX19-26854X" target="_blank" >GX19-26854X: Concert of lipids, ions, and proteins in cell membrane dynamics and function</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2020

Confidentiality

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

Name of the periodical

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Volume of the periodical

16

Issue of the periodical within the volume

1

Country of publishing house

US - UNITED STATES

Number of pages

11

Pages from-to

677-687

UT code for WoS article

000508474800053

EID of the result in the Scopus database

2-s2.0-85076565536