OPLS force field - Revision history

Carl McBride: Slight tidy

2015-11-22T11:31:30Z

Slight tidy

← Older revision		Revision as of 13:31, 22 November 2015
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	{{Stub-general}}		{{Stub-general}}
	The '''optimized potentials for liquid simulations''' (OPLS) [[Force fields \|force-field]] ~~was developed for the simulation~~		The '''optimized potentials for liquid simulations''' (OPLS) [[Force fields \|force-field]]
	~~of [[proteins]] and other organic liquids.~~		<ref>[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657-1666 (1988)]</ref>
	~~====References====~~		<ref>[http://dx.doi.org/10.1002/jcc.540140207 William L. Jorgensen and Toan B. Nguyen "Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions", Journal of Computational Chemistry '''14''' pp. 195-205 (1993)]</ref>
	#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]		was developed for the simulation of [[proteins]] and other organic liquids.
	#[http://dx.doi.org/10.1002/jcc.540140207 William L. Jorgensen and Toan B. Nguyen "Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions", Journal of Computational Chemistry '''14''' pp. 195 - 205 (1993)]
	==OPLS-all atom==		==OPLS-all atom==
	(OPLS-AA)		(OPLS-AA) <ref>[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955-1970 (1997)]</ref>
			<ref>[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225-11236 (1996)]
			and [http://pubs.acs.org/subscribe/journals/jacsat/suppinfo/118/i45/ja9621760/ja11225.pdf Electronic Supporting Information]</ref>
	====Form of the force field====		====Form of the force field====
	Bond stretching		Bond stretching
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	0.5 & ; & {\rm {if}}~~ i,j = 1,4 \\		0.5 & ; & {\rm {if}}~~ i,j = 1,4 \\
	1 & ; & {\rm {otherwise}} \end{array} \right. </math>		1 & ; & {\rm {otherwise}} \end{array} \right. </math>
	====References====		==References==
	#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]		<references/>
	#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]
	~~##[http://pubs.acs.org/subscribe/journals/jacsat/suppinfo/118/i45/ja9621760~~/~~ja11225.pdf Electronic Supporting Information]~~
	[[category:force fields]]		[[category:force fields]]

Nice and Tidy: OPLS moved to OPLS force field

2010-03-05T13:01:10Z

OPLS moved to OPLS force field

← Older revision	Revision as of 15:01, 5 March 2010
(No difference)

Carl McBride at 14:49, 6 November 2007

2007-11-06T14:49:09Z

← Older revision		Revision as of 16:49, 6 November 2007
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	==OPLS-all atom==		==OPLS-all atom==
	(OPLS-AA)		(OPLS-AA)
	===Form of the force field===		====Form of the force field====
	Bond stretching		Bond stretching
	:<math>E_{\rm {bond}} = \sum_{\rm {bonds}} K_r \left(r-r_{eq}\right)^2</math>		:<math>E_{\rm {bond}} = \sum_{\rm {bonds}} K_r \left(r-r_{eq}\right)^2</math>
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	:<math>E(\phi) = \frac{V_1}{2} \left[ 1 + \cos (\phi +f1)\right] + \frac{V_2}{2} \left[ 1 - \cos (2\phi +f2)\right] + \frac{V_3}{2} \left[ 1 + \cos (3\phi +f3)\right]</math>		:<math>E(\phi) = \frac{V_1}{2} \left[ 1 + \cos (\phi +f1)\right] + \frac{V_2}{2} \left[ 1 - \cos (2\phi +f2)\right] + \frac{V_3}{2} \left[ 1 + \cos (3\phi +f3)\right]</math>
	Non-bonded		Non-bonded
	:<math>E_{ab} = \sum_i^{\rm {on~a}}\sum_j^{\rm {on~b}} \left[ \frac{q_i q_j e^2}{r_{ij}} + 4\epsilon_{ij} \left( \frac{\sigma_{ij}^{12}}{r_{ij}^{12}}-\frac{\sigma_{ij}^{6}}{r_{ij}^{6}}\right)\right]f_{ij}</math>		:<math>E_{ab} = \sum_i^{\rm {on~a}}\sum_j^{\rm {on~b}} \left[ \frac{q_i q_j e^2}{r_{ij}} + 4\epsilon_{ij} \left( \frac{\sigma_{ij}^{12}}{r_{ij}^{12}}-\frac{\sigma_{ij}^{6}}{r_{ij}^{6}}\right)\right]f_{ij}, ~~~~f_{ij} = \left\{ \begin{array}{lll}
			0.5 & ; & {\rm {if}}~~ i,j = 1,4 \\
			1 & ; & {\rm {otherwise}} \end{array} \right. </math>
	====References====		====References====
	#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]		#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]

Carl McBride at 14:45, 6 November 2007

2007-11-06T14:45:12Z

← Older revision		Revision as of 16:45, 6 November 2007
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	==OPLS-all atom==		==OPLS-all atom==
	(OPLS-AA)		(OPLS-AA)
			===Form of the force field===
			Bond stretching
			:<math>E_{\rm {bond}} = \sum_{\rm {bonds}} K_r \left(r-r_{eq}\right)^2</math>
			Angle bending
			:<math>E_{\rm {angle}} = \sum_{\rm {angles}} K_\theta \left(\theta-\theta_{eq}\right)^2</math>
			Torsion
			:<math>E(\phi) = \frac{V_1}{2} \left[ 1 + \cos (\phi +f1)\right] + \frac{V_2}{2} \left[ 1 - \cos (2\phi +f2)\right] + \frac{V_3}{2} \left[ 1 + \cos (3\phi +f3)\right]</math>
			Non-bonded
			:<math>E_{ab} = \sum_i^{\rm {on~a}}\sum_j^{\rm {on~b}} \left[ \frac{q_i q_j e^2}{r_{ij}} + 4\epsilon_{ij} \left( \frac{\sigma_{ij}^{12}}{r_{ij}^{12}}-\frac{\sigma_{ij}^{6}}{r_{ij}^{6}}\right)\right]f_{ij}</math>
	====References====		====References====
	#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]		#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]

Carl McBride: /* References */

2007-11-06T14:27:18Z

References

← Older revision		Revision as of 16:27, 6 November 2007
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	#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]		#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]
	#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]		#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]
			##[http://pubs.acs.org/subscribe/journals/jacsat/suppinfo/118/i45/ja9621760/ja11225.pdf Electronic Supporting Information]
	[[category:force fields]]		[[category:force fields]]

Carl McBride at 12:25, 6 November 2007

2007-11-06T12:25:07Z

← Older revision		Revision as of 14:25, 6 November 2007
Line 1:		Line 1:
	{{Stub-general}}		{{Stub-general}}
	The '''optimized potentials for liquid simulations''' (OPLS) force-~~filed~~ was developed for the simulation		The '''optimized potentials for liquid simulations''' (OPLS) [[Force fields \|force-field]] was developed for the simulation
	of proteins and other organic liquids.		of [[proteins]] and other organic liquids.
	====References====		====References====
	#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]		#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]

Carl McBride at 11:41, 6 November 2007

2007-11-06T11:41:13Z

← Older revision		Revision as of 13:41, 6 November 2007
Line 2:		Line 2:
	The '''optimized potentials for liquid simulations''' (OPLS) force-filed was developed for the simulation		The '''optimized potentials for liquid simulations''' (OPLS) force-filed was developed for the simulation
	of proteins and other organic liquids.		of proteins and other organic liquids.
			====References====
	==References==
	#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]		#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]
	#[http://dx.doi.org/10.1002/jcc.540140207 William L. Jorgensen and Toan B. Nguyen "Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions", Journal of Computational Chemistry '''14''' pp. 195 - 205 (1993)]		#[http://dx.doi.org/10.1002/jcc.540140207 William L. Jorgensen and Toan B. Nguyen "Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions", Journal of Computational Chemistry '''14''' pp. 195 - 205 (1993)]
			==OPLS-all atom==
			(OPLS-AA)
			====References====
			#[http://www3.interscience.wiley.com/cgi-bin/abstract/48444/ABSTRACT Wolfgang Damm, Antonio Frontera, Julian Tirado-Rives and William L. Jorgensen "OPLS all-atom force field for carbohydrates", Journal of Computational Chemistry '''18''' pp. 1955 - 1970 (1997)]
	#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]		#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]
	[[category:force fields]]		[[category:force fields]]

Carl McBride: /* References */

2007-11-06T11:29:04Z

References

← Older revision		Revision as of 13:29, 6 November 2007
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	==References==		==References==
	#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]		#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]
			#[http://dx.doi.org/10.1002/jcc.540140207 William L. Jorgensen and Toan B. Nguyen "Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions", Journal of Computational Chemistry '''14''' pp. 195 - 205 (1993)]
	#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]		#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]
	[[category:force fields]]		[[category:force fields]]

Nice and Tidy at 13:19, 15 October 2007

2007-10-15T13:19:34Z

← Older revision		Revision as of 15:19, 15 October 2007
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			{{Stub-general}}
	The '''optimized potentials for liquid simulations''' (OPLS) force-filed was developed for the simulation		The '''optimized potentials for liquid simulations''' (OPLS) force-filed was developed for the simulation
	of proteins and other organic liquids.		of proteins and other organic liquids.

Carl McBride: New page: The '''optimized potentials for liquid simulations''' (OPLS) force-filed was developed for the simulation of proteins and other organic liquids. ==References== #[http://dx.doi.org/10.1021...

2007-03-22T12:53:22Z

New page: The '''optimized potentials for liquid simulations''' (OPLS) force-filed was developed for the simulation of proteins and other organic liquids. ==References== #[http://dx.doi.org/10.1021...

New page

The '''optimized potentials for liquid simulations''' (OPLS) force-filed was developed for the simulation
of proteins and other organic liquids.

==References==
#[http://dx.doi.org/10.1021/ja00214a001 William L. Jorgensen and Julian Tirado-Rives "The OPLS (optimized potentials for liquid simulations) potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin", Journal of the American Chemical Society '''110''' pp. 1657 - 1666 (1988)]
#[http://dx.doi.org/10.1021/ja9621760 William L. Jorgensen, David S. Maxwell, and Julian Tirado-Rives "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids", Journal of the American Chemical Society '''118''' pp. 11225 - 11236 (1996)]
[[category:force fields]]