Deflagration - Revision history

85.193.194.118: Insurance company is a very unreliable source of any definition. The "better" definition, the more money.

2014-12-15T04:39:12Z

Insurance company is a very unreliable source of any definition. The "better" definition, the more money.

← Older revision		Revision as of 06:39, 15 December 2014
Line 1:		Line 1:
	~~{{other uses\|Amber (disambiguation)}}~~		Jerrie Swoboda is what you can call me and I totally dig whom name. Managing people is my time job now. As a girl what I do like is to have croquet but I can not make it my field really. My wife and I chose to live a life in Massachusetts. Go to my web to find out more: http://circuspartypanama.com<br><br>my web site ... [http://circuspartypanama.com clash of clans hacker download]
	~~[[File:Bond stretching energy.png\|thumb\|right\|AMBER~~ is ~~used to minimize the bond stretching energy of this [[ethane]] molecule.]]~~

	'''AMBER''' (an [[acronym]] for '''Assisted Model Building with Energy Refinement''') is a family of [[Force field (chemistry)\|force fields]] for [[molecular dynamics]] of [[biomolecules]] originally developed by [[Peter Kollman]]'s group at the [[University of California, San Francisco]]. '''AMBER''' is also the name ~~for the molecular dynamics software [[Software package (installation)\|package]] that simulates these force fields~~. It is maintained by an active collaboration between David Case at [[Rutgers University]], Tom Cheatham at the [[University of Utah]], Tom Darden at NIEHS, Ken Merz at Florida, [[Carlos Simmerling]] at [[State University of New York at Stony Brook\|Stony Brook University]], Ray Luo at [[UC Irvine]], and Junmei Wang at Encysive Pharmaceuticals.

	~~== Force field ==~~
	~~The term "AMBER [[Force field (chemistry)\|force field]]" generally refers to the functional form used by the family of AMBER force fields~~. ~~This form includes~~ a ~~number of parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.~~

	~~=== Functional form ===~~
	~~The functional form of the AMBER force field~~ is<ref name="Cornell1995">{{cite journal \|author=Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA \|title=A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules \|journal=J. Am. Chem. Soc. \|volume=117 \|pages=5179–5197 \|year=1995 \|doi=10.1021/ja00124a002}}</ref>
	~~:<math>~~
	~~V(r^N)=\sum_\text{bonds} k_b (l-l_0)^2 + \sum_\text{angles} k_a (\theta - \theta_0)^2</math>~~
	~~<blockquote>~~
	~~<math>+ \sum_\text{torsions} \sum_n \frac{1}{2} V_n [1+\cos(n \omega- \gamma)]</math>~~
	<math>+\sum_{j=1} ^{N-1} \sum_{i=j+1} ^N f_{ij}\biggl\{\epsilon_{ij}\biggl[\left(\frac{r_{0ij}}{r_{ij}} \right)^{12} - 2\left(\frac{r_{0ij}}{r_{ij}} \right)^{6} \biggr]+ \frac{q_iq_j}{4\pi \epsilon_0 r_{ij}}\biggr\}
	~~</math>~~
	~~</blockquote>~~
	~~Note that despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential with respect~~ to ~~position.~~

	~~The meanings of right hand side [[term (mathematics)\|terms]] are:~~
	* First term ([[sum]]ming over bonds): represents the energy between covalently bonded atoms. This harmonic (ideal spring) force is a good approximation near the equilibrium bond length, but ~~becomes increasingly poor as atoms separate~~.
	* Second term (summing over angles): represents the energy due to ~~the geometry of electron orbitals involved~~ in ~~covalent bonding~~.
	* Third term (summing over torsions): represents the energy for twisting a bond due to ~~bond order (e.g. double bonds) and neighboring bonds or lone pairs of electrons. Note that a single bond may have~~ more ~~than one of these terms, such that the total torsional energy is expressed as a [[Fourier series]].~~
	* Fourth term (double summation over <math>i</math> and <math>j</math>): represents the non-bonded energy between all atom pairs, which can be decomposed into [[van der Waals force\|van der Waals]] (first term of summation) and [[electrostatics\|electrostatic]] (second term of summation) energies.

	~~The form of the van der Waals energy is calculated using the equilibrium distance (<math> r_{0ij} <~~/~~math>) and well depth (<math> \epsilon <~~/~~math>)~~. ~~The factor of~~ <~~math~~>2<~~/math~~> ensures that the equilibrium distance is <math> r_{0ij} </math>. The energy is sometimes reformulated in terms of <math>\sigma</math>, where <math> r_{0ij} = 2^{1/6}(\sigma)</math>, as used e.g. in the implementation of the softcore potentials.

	The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in an atom can be represented by a single point charge (or in the case of parameter sets that employ lone pairs, a small number of point charges.)

	~~=== Parameter sets ===~~
	To use the AMBER force field, it is necessary to have values for the parameters of the force field (e.g. force constants, equilibrium bond lengths and angles, charges). A fairly large number of these parameter sets exist, and are described in detail in the AMBER software user manual. Each parameter set has a name, and provides parameters for certain types of molecules.
	*Peptide, protein and nucleic acid parameters are provided by parameter sets with names beginning with "ff" and containing a two digit year number, for instance "ff99".
	*GAFF (General AMBER force field) provides parameters for small organic molecules to facilitate simulations of drugs and small molecule ligands in conjunction with biomolecules.
	*The GLYCAM force fields have been developed by Rob Woods for simulating carbohydrates.

	~~== Software ==~~
	The AMBER software suite provides a set of programs for applying the AMBER forcefields to simulations of biomolecules. It is written in [[Fortran 90]] and [[C (programming language)\|C]] with support for most major [[Unix-like]] systems and [[compilers]]. Development is conducted by a loose association of mostly academic labs. New versions are generally released in the spring of even numbered years; AMBER 10 was released in April 2008. The software is available under a site~~-license agreement, which includes full source, currently priced at US$400 for non-commercial and US$20,000 for commercial organizations~~.

	~~=== Programs ===~~
	* '''LEaP''' is used for preparing input files for the simulation programs
	* '''Antechamber''' automates the process of parameterizing small organic molecules using GAFF
	* '''SANDER''' (Simulated Annealing with NMR-Derived Energy Restraints) is the central simulation program and provides facilities for energy minimization and molecular dynamics with a wide variety of options
	* '''pmemd''' is a somewhat more feature-limited reimplementation of sander by Bob Duke. ~~It was designed with parallel processing in mind and has significantly better performance than sander when running on more than 8–16 processors~~
	* '''nmode''' calculates normal modes
	* '''ptraj''' provides facilities for numerical analysis of simulation results. ~~AMBER does not include visualization capabilities; visualization is commonly performed with [[Visual Molecular Dynamics\|VMD]].~~
	* '''MM-PBSA''' allows for implicit solvent calculations on snap shots from molecular dynamics simulations

	~~== See also ==~~
	~~{{columns-list\|2\|~~
	* [[List of software for molecular mechanics modeling]]
	* [[Force field implementation]]
	* [[Molecular dynamics]]
	* [[Molecular geometry]]
	* [[Molecular design software]]
	* [[Molecular mechanics]]
	* [[MDynaMix]]
	* [[Ascalaph Designer]]
	* [[BOSS (molecular mechanics)\|BOSS]]
	* [[CHARMM]]
	* [[GROMACS]]
	* [[OPLS]]
	* [[Yasara]]
	* [[Folding@home]]
	}}

	~~== References ==~~
	~~{{reflist}}~~
	~~===Further reading===<!-- These should be moved inline. -->~~
	* {{cite journal \|author=Duan, ''et al.'' \|last2=Wu \|first2=Chun \|last3=Chowdhury \|first3=Shibasish \|last4=Lee \|first4=Mathew C. \|last5=Xiong \|first5=Guoming \|last6=Zhang \|first6=Wei \|last7=Yang \|first7=Rong \|last8=Cieplak \|first8=Piotr \|last9=Luo \|first9=Ray \|displayauthors=8\|title=A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations \|journal=J Computational Chemistry \|volume=24 \|issue=16 \|pages=1999–2012 \|year=2003 \|doi=10.1002/jcc.10349}}

	~~== External links ==~~
	* [http://~~ambermd~~.~~org/ AMBER website]~~
	* [http://amber.ch.ic.ac.uk/archive/ AMBER mailing list archive]

	~~[[Category:Fortran software]]~~
	~~[[Category:Molecular dynamics software]]~~
	~~[[Category:Force fields]~~]

210.212.211.178 at 07:08, 29 December 2013

2013-12-29T07:08:42Z

← Older revision		Revision as of 09:08, 29 December 2013
Line 1:		Line 1:
	~~Greetings~~. ~~The author~~'s name is ~~Aretha McKean~~ and ~~she or he totally loves~~ this ~~determine~~. ~~One~~ of ~~factors I love most~~ is ~~marquetry~~ and i~~'m trying prospects~~ a ~~work~~. ~~Nevada~~ has ~~always~~ been ~~my home~~. ~~Distributing production will be~~ the he provides ~~an impressive living~~.<br>~~<br>Also visit my web blog~~: [http://~~google~~.~~com caring for your ipad~~]		{{other uses\|Amber (disambiguation)}}
			[[File:Bond stretching energy.png\|thumb\|right\|AMBER is used to minimize the bond stretching energy of this [[ethane]] molecule.]]

			'''AMBER''' (an [[acronym]] for '''Assisted Model Building with Energy Refinement''') is a family of [[Force field (chemistry)\|force fields]] for [[molecular dynamics]] of [[biomolecules]] originally developed by [[Peter Kollman]]'s group at the [[University of California, San Francisco]]. '''AMBER''' is also the name for the molecular dynamics software [[Software package (installation)\|package]] that simulates these force fields. It is maintained by an active collaboration between David Case at [[Rutgers University]], Tom Cheatham at the [[University of Utah]], Tom Darden at NIEHS, Ken Merz at Florida, [[Carlos Simmerling]] at [[State University of New York at Stony Brook\|Stony Brook University]], Ray Luo at [[UC Irvine]], and Junmei Wang at Encysive Pharmaceuticals.

			== Force field ==
			The term "AMBER [[Force field (chemistry)\|force field]]" generally refers to the functional form used by the family of AMBER force fields. This form includes a number of parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.

			=== Functional form ===
			The functional form of the AMBER force field is<ref name="Cornell1995">{{cite journal \|author=Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA \|title=A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules \|journal=J. Am. Chem. Soc. \|volume=117 \|pages=5179–5197 \|year=1995 \|doi=10.1021/ja00124a002}}</ref>
			:<math>
			V(r^N)=\sum_\text{bonds} k_b (l-l_0)^2 + \sum_\text{angles} k_a (\theta - \theta_0)^2</math>
			<blockquote>
			<math>+ \sum_\text{torsions} \sum_n \frac{1}{2} V_n [1+\cos(n \omega- \gamma)]</math>
			<math>+\sum_{j=1} ^{N-1} \sum_{i=j+1} ^N f_{ij}\biggl\{\epsilon_{ij}\biggl[\left(\frac{r_{0ij}}{r_{ij}} \right)^{12} - 2\left(\frac{r_{0ij}}{r_{ij}} \right)^{6} \biggr]+ \frac{q_iq_j}{4\pi \epsilon_0 r_{ij}}\biggr\}
			</math>
			</blockquote>
			Note that despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential with respect to position.

			The meanings of right hand side [[term (mathematics)\|terms]] are:
			* First term ([[sum]]ming over bonds): represents the energy between covalently bonded atoms. This harmonic (ideal spring) force is a good approximation near the equilibrium bond length, but becomes increasingly poor as atoms separate.
			* Second term (summing over angles): represents the energy due to the geometry of electron orbitals involved in covalent bonding.
			* Third term (summing over torsions): represents the energy for twisting a bond due to bond order (e.g. double bonds) and neighboring bonds or lone pairs of electrons. Note that a single bond may have more than one of these terms, such that the total torsional energy is expressed as a [[Fourier series]].
			* Fourth term (double summation over <math>i</math> and <math>j</math>): represents the non-bonded energy between all atom pairs, which can be decomposed into [[van der Waals force\|van der Waals]] (first term of summation) and [[electrostatics\|electrostatic]] (second term of summation) energies.

			The form of the van der Waals energy is calculated using the equilibrium distance (<math> r_{0ij} </math>) and well depth (<math> \epsilon </math>). The factor of <math>2</math> ensures that the equilibrium distance is <math> r_{0ij} </math>. The energy is sometimes reformulated in terms of <math>\sigma</math>, where <math> r_{0ij} = 2^{1/6}(\sigma)</math>, as used e.g. in the implementation of the softcore potentials.

			The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in an atom can be represented by a single point charge (or in the case of parameter sets that employ lone pairs, a small number of point charges.)

			=== Parameter sets ===
			To use the AMBER force field, it is necessary to have values for the parameters of the force field (e.g. force constants, equilibrium bond lengths and angles, charges). A fairly large number of these parameter sets exist, and are described in detail in the AMBER software user manual. Each parameter set has a name, and provides parameters for certain types of molecules.
			*Peptide, protein and nucleic acid parameters are provided by parameter sets with names beginning with "ff" and containing a two digit year number, for instance "ff99".
			*GAFF (General AMBER force field) provides parameters for small organic molecules to facilitate simulations of drugs and small molecule ligands in conjunction with biomolecules.
			*The GLYCAM force fields have been developed by Rob Woods for simulating carbohydrates.

			== Software ==
			The AMBER software suite provides a set of programs for applying the AMBER forcefields to simulations of biomolecules. It is written in [[Fortran 90]] and [[C (programming language)\|C]] with support for most major [[Unix-like]] systems and [[compilers]]. Development is conducted by a loose association of mostly academic labs. New versions are generally released in the spring of even numbered years; AMBER 10 was released in April 2008. The software is available under a site-license agreement, which includes full source, currently priced at US$400 for non-commercial and US$20,000 for commercial organizations.

			=== Programs ===
			* '''LEaP''' is used for preparing input files for the simulation programs
			* '''Antechamber''' automates the process of parameterizing small organic molecules using GAFF
			* '''SANDER''' (Simulated Annealing with NMR-Derived Energy Restraints) is the central simulation program and provides facilities for energy minimization and molecular dynamics with a wide variety of options
			* '''pmemd''' is a somewhat more feature-limited reimplementation of sander by Bob Duke. It was designed with parallel processing in mind and has significantly better performance than sander when running on more than 8–16 processors
			* '''nmode''' calculates normal modes
			* '''ptraj''' provides facilities for numerical analysis of simulation results. AMBER does not include visualization capabilities; visualization is commonly performed with [[Visual Molecular Dynamics\|VMD]].
			* '''MM-PBSA''' allows for implicit solvent calculations on snap shots from molecular dynamics simulations

			== See also ==
			{{columns-list\|2\|
			* [[List of software for molecular mechanics modeling]]
			* [[Force field implementation]]
			* [[Molecular dynamics]]
			* [[Molecular geometry]]
			* [[Molecular design software]]
			* [[Molecular mechanics]]
			* [[MDynaMix]]
			* [[Ascalaph Designer]]
			* [[BOSS (molecular mechanics)\|BOSS]]
			* [[CHARMM]]
			* [[GROMACS]]
			* [[OPLS]]
			* [[Yasara]]
			* [[Folding@home]]
			}}

			== References ==
			{{reflist}}
			===Further reading===<!-- These should be moved inline. -->
			* {{cite journal \|author=Duan, ''et al.'' \|last2=Wu \|first2=Chun \|last3=Chowdhury \|first3=Shibasish \|last4=Lee \|first4=Mathew C. \|last5=Xiong \|first5=Guoming \|last6=Zhang \|first6=Wei \|last7=Yang \|first7=Rong \|last8=Cieplak \|first8=Piotr \|last9=Luo \|first9=Ray \|displayauthors=8\|title=A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations \|journal=J Computational Chemistry \|volume=24 \|issue=16 \|pages=1999–2012 \|year=2003 \|doi=10.1002/jcc.10349}}

			== External links ==
			* [http://ambermd.org/ AMBER website]
			* [http://amber.ch.ic.ac.uk/archive/ AMBER mailing list archive]

			[[Category:Fortran software]]
			[[Category:Molecular dynamics software]]
			[[Category:Force fields]]

216.31.246.186: /* Applications */

2012-08-23T01:03:45Z

Applications

New page

Greetings. The author's name is Aretha McKean and she or he totally loves this determine. One of factors I love most is marquetry and i'm trying prospects a work. Nevada has always been my home. Distributing production will be the he provides an impressive living.<br><br>Also visit my web blog: [http://google.com caring for your ipad]