Abstract
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].
Highlights
Dataset of molecular dynamics simulation trajectories of amino-acid solutions with various force fields, water models and modified force field parameters
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
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]
Summary
Data enable understanding of the influence of force field parameters and water models on the outcome from the generated molecular dynamics trajectories. The simulations with changed parameters of the force field are in folder CHANGED_PAR. These two main folders with trajectories contain directories named by amino-acid three letter code. Raw data from molecular dynamics using seven force field-water model combination. We provide trajectories for glycine (GLY), alanine (ALA), proline (PRO), threonine (THR), leucine (LEU), glutamine (GLN), histidine (HIS) and tyrosine (TYR) for seven force field-water model combinations. FF-NAME stands for “force field name”: OPLS, GROMACS, AMBER, CHARMM, CHARMM19 WM-NAME stands for “water model name”: SPCE∗, TIP3P∗ ∗where accessible
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