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The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules

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Summary

A new program for molecular dynamics (MD) simulation and energy refinement of biological macromolecules, OPAL, is introduced. Combined with the supporting program TRAJEC for the analysis of MD trajectories, OPAL affords high efficiency and flexibility for work with diferent force fields, and offers a user-friendly interface and extensive trajectory analysis capabilities. Salient features are computational speeds of up to 1.5 GFlops on vector supercomputers such as the NEC SX-3, ellipsoidal boundaries to reduce the system size for studies in explicit solvents, and natural treatment of the hydrostatic pressure. Practical applications of OPAL are illustrated with MD simulations of pure water, energy minimization of the NMR structure of the mixed disulfide of a mutant E. coli glutaredoxin with glutathione in different solvent models, and MD simulations of a small protein, pheromone Er-2, using either instantaneous or time-averaged NMR restraints, or no restraints.

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Abbreviations

D:

diffusion constant in cm2/s

Er-2:

pheromone 2 from Euplotes raikovi

GFlop:

one billion floating point operations per second

Grx(C14S)-SG:

mixed disulfide between a mutant E. coli glutaredoxin, with Cys14 replaced by Ser, and glutathione

MD:

molecular dynamics

NOE:

nuclear Overhauser enhancement

rmsd:

root-mean-square deviation

ρ:

density in g/cm3

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Luginbühl, P., Güntert, P., Billeter, M. et al. The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules. J Biomol NMR 8, 136–146 (1996). https://doi.org/10.1007/BF00211160

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