GROMOS force field results

All simulations discussed so far have been performed using one particular force field, the GROMOS G53A5 force field [99]. Because it is well known that the choice of the force field has a strong impact on the results of MD simulations, we performed force probe MD simulations of the tetra-loop calix[4]arene dimer using three different frequently used force fields [100]. The most important... 

MD simulations provide a detailed insight in the behavior of molecular systems in both space and time, with ranges of up to nanometers and nanoseconds attainable for a system of the size of a CYP enzyme in solution. However, MD simulations are based on empirical molecular mechanics (MM) force field descriptions of interactions in the system, and therefore depend directly on the quality of the force field parameters (92). Commonly used MD programs for CYPs are AMBER (93), CHARMM (94), GROMOS (95), and GROMACS (96), and results seem to be comparable between methods (also listed in Table 2). For validation, direct comparisons between measured parameters and parameters calculated from MD simulations are possible, e.g., for fluorescence (97) and NMR (cross-relaxation) (98,99). In many applications where previously only energy minimization would be applied, it is now common to perform one or several MD simulations, as Ludemann et al. and Winn et al. (100-102) performed in studies of substrate entrance and product exit. 

The first important dynamic CyD studies published in 1987 and 1988 were the result of cooperation by the theoreticians van Gunsteren and Koehler with the X-ray specialist Saenger [98, 99, 100, 101, 102]. The aim of these studies was twofold on the one hand, they served the development of the GROMOS force field [103] while on the other they had to show that DSs for such complicated systems as CyDs were feasible. Starting from the experimental structures, these simulations of 15 or 20 ps, very short by today s standards, are of historical interest only. Similarly, the work by Mark et al. [104] of 1994 on free perturbation calculations was mainly devoted to the development of the method. 

Cyclodextrins have had valuable industrial uses for a considerable time, particularly as agents to bind or release volatile molecules. Accurate predictions concerning the selectivity and stability of cyclodextrin-guest complexes are therefore of considerable interest both academically and practically." MD was used to simulate cyclodextrin hydrates" as a test of the applicability of the GROMOS program package to systems beyond proteins and nucleic acids. Other early MD simulations focused on interactions with guests such as enantiomers of methyl-2-chloropropionate. Comparisons between calculated thermodynamic properties for complexes formed by O -cyclodextrin with para-substituted phenols and the results of MM simulations led to improvements in force fields that described the interactions. MM2 simulations were used to support NMR data for the -cyclodextrin inclusion complex with benzoic acid. " The well-known catalytic effect of cyclodextrins has been modeled. For example, the relative rate increase of hydrolysis of S over R phenyl ester stereoisomers in the presence of -cyclodextrin... 

The observation that most common united-atom force fields seem to lead to a density that is too high, led Berger et al. to re-parameterize a force field for DPPC starting with the GROMOS bonded parameters, the OPLS nonbonded parameters and three different sets of partial charges. The Lennard-Jones parameters for the hydrocarbon tails were determined from pentadecane simulations. The final choice of these authors results in a density that agrees within % with the experimental density. ... 

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