Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters

0538173 - ÚFE 2021 RIV DE eng J - Článek v odborném periodiku
Průša, Jiří - Cifra, Michal
Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters.
Data in Brief. Roč. 30, June (2020), č. článku 105483. ISSN 2352-3409
Grant CEP: GA ČR GA18-23597S
Grant ostatní: AV ČR(CZ) SAV-18-11; GA MŠk(CZ) LM2015042
Program: Bilaterální spolupráce
Institucionální podpora: RVO:67985882
Klíčová slova: Amino acid * Biomolecules * Dielectric spectroscopy * Force field * Molecular dynamics
Obor OECD: Electrical and electronic engineering
Způsob publikování: Open access
https://doi.org/10.1016/j.dib.2020.105483

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
Trvalý link: http://hdl.handle.net/11104/0315994