Ammm:Adaptive umbrella sampling: Difference between revisions
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= <span style="background-color: rgb(153,204,255)">The potential energy as the variable for adaptive umbrella sampling </span><br> = | = <span style="background-color: rgb(153,204,255)">The potential energy as the variable for adaptive umbrella sampling </span><br> = | ||
[[Image:Adaptive umbrella sampling.pdf]]<ref>Christian Bartels and Martin Karplus, Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy. J. Phys. Chem. B 1998, 102, 865-880</ref> | [[Image:Adaptive umbrella sampling.pdf |600px]]<ref>Christian Bartels and Martin Karplus, Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy. J. Phys. Chem. B 1998, 102, 865-880</ref> | ||
[[Image:Multidimensional Adaptive Umbrella Sampling Applications to Main Chain and Side Chain Peptide Conformationsjcc 97.pdf]] <ref>Christian Bartels and Martin Karplus, Multidimensional Adaptive Umbrella Sampling Applications to Main Chain and Side Chain Peptide Conformations. Journal of Computational Chemistry, Vol. 18, No. 12, 1450-1462(1997)</ref> | [[Image:Multidimensional Adaptive Umbrella Sampling Applications to Main Chain and Side Chain Peptide Conformationsjcc 97.pdf]] <ref>Christian Bartels and Martin Karplus, Multidimensional Adaptive Umbrella Sampling Applications to Main Chain and Side Chain Peptide Conformations. Journal of Computational Chemistry, Vol. 18, No. 12, 1450-1462(1997)</ref> | ||
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*<span style="font-size: x-large">Extrapolation of the Umbrella Potential: </span> | *<span style="font-size: x-large">Extrapolation of the Umbrella Potential: </span> | ||
[[Image:Umbrella 16.PNG]] | [[Image:Umbrella 16.PNG]] | ||
= <span style="background-color: rgb(153,204,255)">Application:Threonine Dipeptide </span><br> = | = <span style="background-color: rgb(153,204,255)">Application:Threonine Dipeptide </span><br> = | ||
Revision as of 16:00, 10 May 2022
Multicanonical ensemble
Background of adaptive umbrella sampling
- Review of umbrella sampling (more details please refer to Yue's page)
http://water.bme.utexas.edu/wiki/index.php/ABS:Umbrella_sampling_and_WHAM
Umbrella sampling attempts to overcome the sampling problem by modifying the Hamiltonian so that
the unfavorable states are sampled sufficiently. The modification can be written as a perturbation.
- The trial and error method for umbrella sampling
Theory of adaptive umbrella sampling
- Definitions
- The outline of the algorithm:
The potential energy as the variable for adaptive umbrella sampling
The potential energy, in contrast to the commonly used umbrella potentials,
is of particular interest for complex systems because it does not depend on
assumptions about the geometry nor on a knowledge of the important
conformations and transition states that are involved in the equilibration.
- Range of Sampling:
- Extrapolation of the Umbrella Potential:
Application:Threonine Dipeptide
- System setup
- adaptive umbrella sampling runs were performed at 303 K.
- T-min was set equal to 280 K, while T-max was set equal to 2000 K.
- V-min ~ V-max set as -50 to 100 kcal/mol.
- 200 bins.
- The umbrella potential was represented as a linear combination of 40 trigonometric functions
- Results
References
- ↑ Ulrich H.E. Hansmann a, Yuko Okamoto, Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem. Physica A 212 (1994) 415-437
- ↑ MIHALY MEZEI, Adaptive Umbrella Sampling: Self-consistent Determination of the Non-Boltzmann Bias. JOURNAL OF COMPUTATIONAL PHYSICS Vol. 68, No. 1, 1987
- ↑ Christian Bartels and Martin Karplus, Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy. J. Phys. Chem. B 1998, 102, 865-880
- ↑ Christian Bartels and Martin Karplus, Multidimensional Adaptive Umbrella Sampling Applications to Main Chain and Side Chain Peptide Conformations. Journal of Computational Chemistry, Vol. 18, No. 12, 1450-1462(1997)