Defect evolution in ultrathin films of polystyrene-block-polymethylmethacrylate diblock copolymers observed by atomic force microscopy
We track individual defects in the microdomain patterns of cylinder-forming polystyrene-block-polymethylmethacrylate films with atomic force microscopy to elucidate the evolution of diblock domain top...
We track individual defects in the microdomain patterns of cylinder-forming polystyrene-block-polymethylmethacrylate films with atomic force microscopy to elucidate the evolution of diblock domain top...
Stochastic complexity and statistical mechanics
A statistical mechanical formalism based on stochastic complexity is presented. Stochastic complexity is a statistical estimation scheme that uses the principle of minimal description length (MDL). Th...
A statistical mechanical formalism based on stochastic complexity is presented. Stochastic complexity is a statistical estimation scheme that uses the principle of minimal description length (MDL). Th...
Equilibration and sampling in molecular dynamics simulations of biomolecules
J. Chem. Phys. 109, 10115 (1998); doi:10.1063/1.477703
Issue Date: 15 December 1998
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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.
| History: | Received 27 July 1998; accepted 8 October 1998 |
| Permalink: |
http://link.aip.org/link/?JCPSA6/109/10115/1 |
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BibSonomy
KEYWORDS and PACS
molecular biophysics,
digital simulation,
molecular dynamics method,
statistical analysis,
relaxation
- 87.15.He
Biological and medical physics Molecular biophysics Molecular dynamics and conformational changes - 02.70.Ns
Mathematical methods in physics Computational techniques Molecular dynamics and particle methods - 02.50.-r
Mathematical methods in physics Probability theory, stochastic processes, and statistics - 02.60.-x
Mathematical methods in physics Numerical approximation and analysis - YEAR: 1998
RELATED DATABASES
PUBLICATION DATA
0021-9606 (print)
1089-7690 (online)
AIP
REFERENCES (6)
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