Comparison of two force fields by molecular dynamics simulations of glucose crystals: Effect of using ewald sums

Abstract

To compare the GROMOS force field with one designed by Ha et al., molecular dynamics simulations of u-D-glucose anhydrate and monohydrate crystals were performed. Also, the long-range interactions were calculated both with a cutoff approximation and with Ewald summations. The results are compared with results obtained experimentally by neutron and X-ray diffraction. The force-field parameters had been optimized with the cutoff approximation; this apparently led to worse results when the Ewald summations were used. However, in all simulations the symmetry was roughly preserved and the mean atomic coordinates and thermal parameters, bond angles, and dihedrals without hydrogen atoms were rather well reproduced. The dihedrals with hydrogen atoms exhibited conformational transitions, which resulted in a disordered hydrogen bonding scheme. In general, the GROMOS force field performed better than the Ha force field. 0 1993 by John

Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates

“…In agreement with the findings of Kouwijzer et al [17], during the first 20 ps the simulations reached equilibrium, as determined both from the temperatures that had stabilized at 298 ± 1.5 K over this period, and from the energies that had reached equilibrium within that period. Table 1 presents the average crystal dimensions and energies for a series of simulations performed with several charge sets.…”

“…In order to ensure that the motions of each molecule were sensitive only to the force field, we elected not to impose crystallographic symmetry during the simulations. Following the model proposed by Kouwijzer et al [17], we created a crystal that contained 64 molecules (Fig 1). This structure corresponded to a simulation box containing 2 × 2 × 4 crystallographic unit cells [18] and ensured that the use of a 10.5 Å cut-off for non-bonded interactions did not introduce imaging artifacts.…”

Empirical force fields for biological macromolecules: Overview and issues

“…Brady and coworkers have developed models for hexopyranose sugars based on small molecule geometric and vibrational data and on ␣-D-glucopyranose. 289 However, this force field yields incorrect conformational properties for the exocyclic hydroxyl, 290 glycosyl bonds are not treated, and the model is only limited to hydroxyl substituents. More recently, this model has been reoptimized, in part to be consistent with the CHARMM22 protein and CHARMM27 nucleic acid/lipid force fields and to yield improved conformational properties for the exocyclic hydroxyl group.…”

Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field

“…267,268 For completeness, it should be mentioned that ab initio MD simulations of carbohydrates have also been performed. 98,269,270 The most commonly used force fields have been discussed in recent reviews, 217,219,271,272 and a number of more or less extensive force field comparisons (against vacuum, 233,273,274 solid state 275,276 or solution 273,277,278 data) have also been undertaken.…”