Electronic Resource
College Park, Md.
:
American Institute of Physics (AIP)
The Journal of Chemical Physics
109 (1998), S. 10115-10117
ISSN:
1089-7690
Source:
AIP Digital Archive
Topics:
Physics
,
Chemistry and Pharmacology
Notes:
In this Communication we analyze the relaxation to equilibrium of a biomolecule and its sampling of the equilibrium ensemble, by using simple collective observables. We demonstrate that the customary use of the root mean square positional deviation parameter from the initial structure of a molecular dynamics trajectory, to determine the attainment of a stationary state in a simulation of biomolecules, necessarily leads to an overestimation of the relaxation time; this causes a loss of precious data that otherwise could be used in the calculation of equilibrium properties. A simple and reliable alternative is suggested, by computing the root mean square deviation from several different reference conformations along the trajectory. © 1998 American Institute of Physics.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1063/1.477703
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