title: Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.
abstract: We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8].
authors.affiliation: Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany.
authors.forename: F
authors.initials: F
authors.lastname: Vitalini
authors.affiliation: Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany.
authors.forename: F
authors.initials: F
authors.lastname: Noé
authors.affiliation: Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany.
authors.forename: B G
authors.initials: BG
authors.lastname: Keller
keywords: Amino acid; Force field; Molecular dynamics