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

. 2020 Jun ; 30 () : 105483. [epub] 20200408

Status PubMed-not-MEDLINE Jazyk angličtina Země Nizozemsko Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid32368577
Odkazy

PubMed 32368577
PubMed Central PMC7184122
DOI 10.1016/j.dib.2020.105483
PII: S2352-3409(20)30377-2
Knihovny.cz E-zdroje

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].

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