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| - Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of thePotential Energy
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| Abstract
| - An adaptive umbrella sampling molecular dynamicsalgorithm based on the potential energy is introduced toreduce the simulation time required for deriving equilibrium propertiesof molecular systems. The potentialenergy, in contrast to the commonly used umbrella potentials, is ofparticular interest for complex systemsbecause it does not depend on assumptions about the geometry nor on aknowledge of the importantconformations and transition states that are involved in theequilibration. The method is illustrated by applyingit to the threonine dipeptide and to met-Enkephalin. For thethreonine dipeptide, potentials of mean force forall dihedral angles of the system are derived from a single 10 ns run.The accuracy of the potentials isconfirmed by comparison with previous results. Met-Enkephalin isfound to sample several differentconformations at 300 K. Three representative structures are usedto cluster the dominant conformations.Equilibrium distributions of dihedral angles and the distancebetween the two termini are calculated. Theprecision of the results is analyzed, and the utility of the proposedadaptive umbrella sampling method isdiscussed.
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