Ammm:Adaptive umbrella sampling - Revision history

Admin at 16:01, 10 May 2022

2022-05-10T16:01:04Z

← Older revision		Revision as of 16:01, 10 May 2022
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	[[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: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 \|600px] <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>

	<span style="font-size: medium"> </span><span style="font-size: large"> The potential energy, in contrast to the commonly used umbrella potentials, </span>		<span style="font-size: medium"> </span><span style="font-size: large"> The potential energy, in contrast to the commonly used umbrella potentials, </span>

Admin: /* The potential energy as the variable for adaptive umbrella sampling */

2022-05-10T16:00:20Z

The potential energy as the variable for adaptive umbrella sampling

← Older revision		Revision as of 16:00, 10 May 2022
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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> =

Admin: /* Background of adaptive umbrella sampling */

2022-05-10T15:59:59Z

Background of adaptive umbrella sampling

← Older revision		Revision as of 15:59, 10 May 2022
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	= <span style="background-color: rgb(153,204,255)">Background of adaptive umbrella sampling </span><br> =		= <span style="background-color: rgb(153,204,255)">Background of adaptive umbrella sampling </span><br> =

	[[Image:Adaptive umbrella sampling.pdf]] <ref>MIHALY MEZEI, Adaptive Umbrella Sampling: Self-consistent Determination of the Non-Boltzmann Bias. JOURNAL OF COMPUTATIONAL PHYSICS Vol. 68, No. 1, 1987</ref>		[[Image:Adaptive umbrella sampling.pdf \|500px]] <ref>MIHALY MEZEI, Adaptive Umbrella Sampling: Self-consistent Determination of the Non-Boltzmann Bias. JOURNAL OF COMPUTATIONAL PHYSICS Vol. 68, No. 1, 1987</ref>

	*<span style="font-size: medium">Review of umbrella sampling (more details please refer to Yue's page) </span>		*<span style="font-size: medium">Review of umbrella sampling (more details please refer to Yue's page) </span>
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	*<span style="font-size: large">The trial and error method for umbrella sampling </span>		*<span style="font-size: large">The trial and error method for umbrella sampling </span>

	<br>[[Image:Umbrella 2.PNG]] [[Image:Umbrella 41.PNG]]		<br>[[Image:Umbrella 2.PNG]] [[Image:Umbrella 41.PNG]]

	= <span style="background-color: rgb(153,204,255)">Theory of adaptive umbrella sampling </span><br> =		= <span style="background-color: rgb(153,204,255)">Theory of adaptive umbrella sampling </span><br> =

Admin: Created page with "= Multicanonical ensemble
= 500px 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 Image:Umbrella 22.PNG Image:Umbrella 23.PNG Image:Umbrella 24.PNG = Background of adaptive umbrella sam..."

2022-05-10T15:59:42Z

Created page with "= Multicanonical ensemble = 500px <ref>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</ref> Image:Umbrella 22.PNG Image:Umbrella 23.PNG Image:Umbrella 24.PNG = Background of adaptive umbrella sam..."

New page

= Multicanonical ensemble =

[[Image:Multicanonical.pdf |500px]] <ref>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</ref>

[[Image:Umbrella 22.PNG]] [[Image:Umbrella 23.PNG]] [[Image:Umbrella 24.PNG]]

= Background of adaptive umbrella sampling =

[[Image:Adaptive umbrella sampling.pdf]] <ref>MIHALY MEZEI, Adaptive Umbrella Sampling: Self-consistent Determination of the Non-Boltzmann Bias. JOURNAL OF COMPUTATIONAL PHYSICS Vol. 68, No. 1, 1987</ref>

*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 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. 

[[Image:Umbrella 1.PNG]]

*The trial and error method for umbrella sampling 

 [[Image:Umbrella 2.PNG]] [[Image:Umbrella 41.PNG]]

= Theory of adaptive umbrella sampling =

*Definitions 

[[Image:Umbrella 52.PNG]]

*The outline of the algorithm: 

[[Image:Umbrella 62.PNG]] [[Image:Umbrella 71.PNG]] [[Image:Umbrella 8.PNG]]

= The potential energy as the variable for adaptive umbrella sampling =

[[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: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>

  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. 

[[Image:Umbrella 9.PNG]]

[[Image:Umbrella 10.PNG]]

[[Image:Umbrella 11.PNG]] [[Image:Umbrella 25.PNG|thumb|right]]

[[Image:Umbrella 12.PNG]]

*Range of Sampling: 

[[Image:Umbrella 13.PNG]]

[[Image:Umbrella 14.PNG]]

[[Image:Umbrella 15.PNG]]

*Extrapolation of the Umbrella Potential: 

[[Image:Umbrella 16.PNG]]

= Application:Threonine Dipeptide =

[[Image:Umbrella 17.PNG]]

*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 

[[Image:Umbrella 18.PNG]]

*Results 

[[Image:Umbrella 19.PNG]]

 [[Image:Umbrella 21.PNG]] 

= References =

''' '''<references />