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Refinement Using Time-Averaged Distance Restraints

NMR-derived structures can be refined with time-averaged NOE distance
restraints (Torda, Scheek, and van Gunsteren, 1990,1989; Pearlman and Kollman, 1991)
using
the TAVErage statement. In this method the NOE restraint potential is
changed so that distance restraints derived from NOE are applied to
the time-average of each distance, rather than each instantaneous
distance. Thus R in Eqs. 20.7,
20.10, 20.12, 20.13
is replaced by an averaged distance

In practice, a slightly different form of the above equation is used
to calculate ; for a discrete number of time points, the
equation becomes

(20.23) |

(20.24) |

The initial values for can be set to either the current distances, , or to the restraint distances, , using the TAVErage RESEt statement (CURRent or CONStraint).

The force associated with each NOE restraint is normally taken to be
the spatial derivative of the energy term, e.g. for a square well
potential,

(20.25) |

(20.26) |

(20.27) |

Note the fourth-power term with respect to ; this may give rise to occasional large forces. To circumvent this problem, Torda, Scheek, and van Gunsteren (1989) proposed an alternative force:

Integrating this force term leads to a time-dependent NOE energy term, hence this force is nonconservative. In X-PLOR the force field can be chosen by setting FORCe to either CONServative (Eq. 20.28) or NONConservative (Eq. 20.29).

X-PLOR can also accumulate running-averages of the distances using the
RAVErage statement. The running-average is calculated from

(20.30) |

(20.31) |

See Section 38.10 for an example for time- and running-averages.

*Xplor-NIH 2024-09-13*