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Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters
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SYSNO ASEP 0538173 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters Author(s) Průša, Jiří (URE-Y)
Cifra, Michal (URE-Y) RID, ORCID, SAINumber of authors 2 Article number 105483 Source Title Data in Brief. - : Elsevier - ISSN 2352-3409
Roč. 30, June (2020)Number of pages 5 s. Publication form Print - P Language eng - English Country DE - Germany Keywords Amino acid ; Biomolecules ; Dielectric spectroscopy ; Force field ; Molecular dynamics Subject RIV JA - Electronics ; Optoelectronics, Electrical Engineering OECD category Electrical and electronic engineering R&D Projects GA18-23597S GA ČR - Czech Science Foundation (CSF) Method of publishing Open access Institutional support URE-Y - RVO:67985882 UT WOS 000542612000019 EID SCOPUS 85083549141 DOI 10.1016/j.dib.2020.105483 Annotation We present molecular dynamics (MD) trajectories of water solutions of eight zwitterionic amino-acids (L- form) glycine (GLY), alanine (ALA), proline (PRO), threonine (THR), leucine (LEU), glutamine (GLN), histidine (HIS) and tyrosine (TYR) using various force field (OPLS-AA, Amber99ff-SB, GROMOS96 54a7, CHARMMI9) and water model (SPC/E, TIP3P) combinations. Additionally, we present OPLS-AA molecular dynamics (MD) trajectories for alanine (ALA), leucine (LEU), glutamine (GLN), and tyrosine (TYR) varying the values of major force field parameters: charge on all amino acid atoms, bond length (all amino acid bonds), Lennard-Jones potential epsilon parameter and stiffness of bond angles. Our data enable to uncover sensitivity of molecular dynamics derived analysis to variation of force field and water models and force field parameters. This data set was used to understand the effect of molecular dynamics parameters on dielectric properties of amino acid solutions Workplace Institute of Radio Engineering and Electronics Contact Petr Vacek, vacek@ufe.cz, Tel.: 266 773 413, 266 773 438, 266 773 488 Year of Publishing 2021 Electronic address https://doi.org/10.1016/j.dib.2020.105483
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