Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters
Status PubMed-not-MEDLINE Jazyk angličtina Země Nizozemsko Médium electronic-ecollection
Typ dokumentu časopisecké články
PubMed
32368577
PubMed Central
PMC7184122
DOI
10.1016/j.dib.2020.105483
PII: S2352-3409(20)30377-2
Knihovny.cz E-zdroje
- Klíčová slova
- Amino acid, Biomolecules, Dielectric spectroscopy, Force field, Molecular dynamics,
- Publikační typ
- časopisecké články MeSH
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, CHARMM19) 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 [1].
Institute of Photonics and Electronics of the Czech Academy of Sciences Prague Czech Republic
University of Chemistry and Technology Prague Czech Republic
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