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].

Adsorption of amino acids on graphene: assessment of current force fields

“…A major deviation in the regions of φ-ψ space sampled is observed for Val, where Amber03w/TIP4P/2005 has much lower sampling near the α-helix and δ-region compared to other amino acids. This is consistent with previous observations [98]. Such a contrast between Val and other amino acids is not observed for the other force fields.…”

“…A notable difference is that the bridge regions (ζ, γ) between the α-helical and β-sheets are sampled more in OPLS-AA/M/TIP3P compared to the other force fields. The overall differences across force fields are qualitatively consistent with those reported by Vitalini et al [98] using µs long simulations. This suggests that our simulations have successfully sampled the key conformational features.…”

“…[40-43, 94, 95] A wellappreciated problem with the earlier versions of Amber, CHARMM, and OPLS is a bias in the structure towards either α-helix or β-sheets. [95][96][97][98] Therefore, these force fields have been revised with updated torsional parameters based on quantum simulations and experimental data (details are provided in SI Section 2). The revision protocols primarily differ in the reference backbone space used for scanning the side chain dihedral space, and the weight factors used to minimize the potential energies determined by molecular and quantum mechanics simulations.…”

Combining enhanced sampling with experiment-directed simulation of the GYG peptide

“…Enhanced sampling technique found a different global minimum at Φ=1 and Ψ=1, in the absence of EDS than in the presence of EDS. Also, PT-WTE without EDS enabled the exploration of a region at Φ=1 and Ψ in interval [-3.14,3.14] radians in figure 2b which is similar to Tyrosine Ramachandran map from Vitalini et al; 47 neither of EDS alone (Fig. 2c), EDS with PT-WTE ( Fig.…”

Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

“…[40-43, 94, 95] A wellappreciated problem with the earlier versions of Amber, CHARMM, and OPLS is a bias in the structure towards either α-helix or β-sheets. [95][96][97][98] Therefore, these force fields have been revised with updated torsional parameters based on quantum simulations and experimental data (details are provided in SI Section 2). The revision protocols primarily differ in the reference backbone space used for scanning the side chain dihedral space, and the weight factors used to minimize the potential energies determined by molecular and quantum mechanics simulations.…”