Parametrisation of time-averaged distance restraints in MD simulations.
Time-averaged restraints in molecular dynamics simulations offer a means to account for the averaging that is implicit in NMR spectroscopic data. We present a systematic investigation of the parameters which characterise time-averaged distance restraints. Using previously published data for a small protein, chymotrypsin inhibitor 2, we identify conditions which can lead to undesirable heating or which grossly distort the dynamics of the system.
Department of Physical Chemistry, ETH Zentrum, CH-8092, Zürich, Switzerland.
A P
AP
Nanzer
W F
WF
van Gunsteren
A E
AE
Torda