SWM4-DP model of water - Revision history

Carl McBride: Removed stub template

2014-01-13T10:14:37Z

Removed stub template

← Older revision		Revision as of 12:14, 13 January 2014
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	~~{{Stub-water}}~~
	The '''SWM4-DP''' model		The '''SWM4-DP''' model
	<ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water based on classical Drude oscillators", Journal of Chemical Physics '''119''' pp. 5185- (2003)]</ref>		<ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water based on classical Drude oscillators", Journal of Chemical Physics '''119''' pp. 5185- (2003)]</ref>

Carl McBride: Added a table for the SWM6 parameters

2014-01-13T10:08:25Z

Added a table for the SWM6 parameters

← Older revision		Revision as of 12:08, 13 January 2014
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	\|}		\|}
	==SWM6==		==SWM6==
	SWM6 <ref>[http://dx.doi.org/10.1063/1.4774577 Wenbo Yu, Pedro E. M. Lopes, Benoît Roux, and Alexander D. MacKerell, Jr. "Six-site polarizable model of water based on the classical Drude oscillator", Journal of Chemical Physics '''138''' 034508 (2013)]</ref>.		The SWM6 <ref>[http://dx.doi.org/10.1063/1.4774577 Wenbo Yu, Pedro E. M. Lopes, Benoît Roux, and Alexander D. MacKerell, Jr. "Six-site polarizable model of water based on the classical Drude oscillator", Journal of Chemical Physics '''138''' 034508 (2013)]</ref> model is a six-site model that adds oxygen lone-pairs (<math>L</math>) to the SWM4-NDP model. The parameters are given by:
			{\| style="width:60%; height:100px" border="1"
			\|-
			\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH (deg)\|\| <math>\angle</math>LOL (deg)\|\| <math>R_{ \mathrm{min, O} }</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e)\|\| q(L) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å)\|\| <math>r_{\mathrm {OL}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)
			\|-
			\| 0.9572 \|\| 104.52 \|\| 101.098\|\| 3.59 \|\| 0.162 \|\| 1.91589 \|\| 0.53070 \|\| -1.1334 \|\| -0.108 \|\| 0.247\|\| 0.315 \|\| -1.62789 \|\| 1000
			\|}
	==References==		==References==
	<references/>		<references/>
	[[category: water]]		[[category: water]]
	[[category: models]]		[[category: models]]

Carl McBride: Added a new table for the SWM4-NDP parameters.

2014-01-13T09:41:54Z

Added a new table for the SWM4-NDP parameters.

← Older revision		Revision as of 11:41, 13 January 2014
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	==Parameters==		==Parameters==
	[[Image:Four_site_water_model.png‎\|center\|300px]]		[[Image:Four_site_water_model.png‎\|center\|300px]]


	{\| style="width:60%; height:100px" border="1"		{\| style="width:60%; height:100px" border="1"
	\|-		\|-
	\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH , deg\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)		\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH (deg)\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)
	\|-		\|-
	\| 0.9572 \|\| 104.52 \|\| 3.1803 \|\| 0.~~210943~~ \|\| -1.~~11466~~ \|\| 0.5537 \|\| -2q(H) \|\| 0.23808 \|\| -q(O) \|\| 1000		\| 0.9572 \|\| 104.52 \|\| 3.1803 \|\| 0.20568 \|\| -1.77185 \|\| 0.5537 \|\| -2q(H) \|\| 0.23808 \|\| -q(O) \|\| 1000
	\|}		\|}

	==SWM4-NDP==		==SWM4-NDP==
	SWM4-NDP <ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>.		The SWM4-NDP model<ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref> is a version that has been re-optimized for negatively charged Drude particles. The parameters are given by:
			{\| style="width:60%; height:100px" border="1"
			\|-
			\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH (deg)\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)
			\|-
			\| 0.9572 \|\| 104.52 \|\| 3.18395 \|\| 0.21094 \|\| 1.71636 \|\| 0.55733 \|\| -2q(H) \|\| 0.24034 \|\| -q(O) \|\| 1000
			\|}
	==SWM6==		==SWM6==
	SWM6 <ref>[http://dx.doi.org/10.1063/1.4774577 Wenbo Yu, Pedro E. M. Lopes, Benoît Roux, and Alexander D. MacKerell, Jr. "Six-site polarizable model of water based on the classical Drude oscillator", Journal of Chemical Physics '''138''' 034508 (2013)]</ref>.		SWM6 <ref>[http://dx.doi.org/10.1063/1.4774577 Wenbo Yu, Pedro E. M. Lopes, Benoît Roux, and Alexander D. MacKerell, Jr. "Six-site polarizable model of water based on the classical Drude oscillator", Journal of Chemical Physics '''138''' 034508 (2013)]</ref>.

24.168.13.79: /* Parameters */

2014-01-13T02:14:16Z

Parameters

← Older revision		Revision as of 04:14, 13 January 2014
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	\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH , deg\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)		\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH , deg\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)
	\|-		\|-
	\| 0.9572 \|\| 104.52 \|\| 3.1803 \|\| 0.~~20568~~ \|\| -1.11466 \|\| 0.5537 \|\| -2q(H) \|\| 0.23808 \|\| -q(O) \|\| 1000		\| 0.9572 \|\| 104.52 \|\| 3.1803 \|\| 0.210943 \|\| -1.11466 \|\| 0.5537 \|\| -2q(H) \|\| 0.23808 \|\| -q(O) \|\| 1000
	\|}		\|}

24.168.13.79: /* Parameters */

2014-01-13T02:12:03Z

Parameters

← Older revision		Revision as of 04:12, 13 January 2014
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	\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH , deg\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)		\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH , deg\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)
	\|-		\|-
	\| 0.9572 \|\| 104.52 \|\| 3.1803 \|\| 0.20568 \|\| -1.~~77185~~ \|\| 0.5537 \|\| -2q(H) \|\| 0.23808 \|\| -q(O) \|\| 1000		\| 0.9572 \|\| 104.52 \|\| 3.1803 \|\| 0.20568 \|\| -1.11466 \|\| 0.5537 \|\| -2q(H) \|\| 0.23808 \|\| -q(O) \|\| 1000
	\|}		\|}

Carl McBride: Added mention of SWM6

2013-04-25T12:17:22Z

Added mention of SWM6

← Older revision		Revision as of 14:17, 25 April 2013
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	==SWM4-NDP==		==SWM4-NDP==
	<ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>		SWM4-NDP <ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>.
			==SWM6==
			SWM6 <ref>[http://dx.doi.org/10.1063/1.4774577 Wenbo Yu, Pedro E. M. Lopes, Benoît Roux, and Alexander D. MacKerell, Jr. "Six-site polarizable model of water based on the classical Drude oscillator", Journal of Chemical Physics '''138''' 034508 (2013)]</ref>.
	==References==		==References==
	<references/>		<references/>
	[[category: water]]		[[category: water]]
	[[category: models]]		[[category: models]]

Carl McBride: Added parameters.

2010-05-05T17:08:17Z

Added parameters.

← Older revision		Revision as of 19:08, 5 May 2010
Line 1:		Line 1:
	{{Stub-water}}		{{Stub-water}}
	The '''SWM4-DP''' model		The '''SWM4-DP''' model
	<ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water based on classical Drude oscillators", Journal of Chemical Physics '''119''' pp. 5185- (2003)]</ref>		<ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water based on classical Drude oscillators", Journal of Chemical Physics '''119''' pp. 5185- (2003)]</ref>
	<ref>[http://dx.doi.org/10.1063/1.1589749 Guillaume Lamoureux and Benoît Roux "Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm", Journal of Chemical Physics '''119''' pp. 3025- (2003)]</ref>		<ref>[http://dx.doi.org/10.1063/1.1589749 Guillaume Lamoureux and Benoît Roux "Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm", Journal of Chemical Physics '''119''' pp. 3025- (2003)]</ref>
	of [[water]].		of [[water]] has a [[TIP4P model of water \| TIP4P]] like structure, as well as incorporating a [[Drude oscillators \| Drude oscillator]].
			==Parameters==
			[[Image:Four_site_water_model.png‎\|center\|300px]]


			{\| style="width:60%; height:100px" border="1"
			\|-
			\| <math>r_{\mathrm {OH}}</math> (Å)\|\| <math>\angle</math>HOH , deg\|\| <math>\sigma</math> (Å)\|\| <math>\epsilon</math> (kcal/mol)\|\| q(O) (e) \|\| q(H) (e) \|\| q(M) (e) \|\| <math>r_{\mathrm {OM}}</math> (Å) \|\| q(Drude) (e) \|\| k(Drude) (kcal/mol/Å<sup>2</sup>)
			\|-
			\| 0.9572 \|\| 104.52 \|\| 3.1803 \|\| 0.20568 \|\| -1.77185 \|\| 0.5537 \|\| -2q(H) \|\| 0.23808 \|\| -q(O) \|\| 1000
			\|}

	==SWM4-NDP==		==SWM4-NDP==
	<ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>		<ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>

Nice and Tidy: SWM4-DP moved to SWM4-DP model of water

2010-02-23T14:47:36Z

SWM4-DP moved to SWM4-DP model of water

← Older revision	Revision as of 16:47, 23 February 2010
(No difference)

Carl McBride: Added another reference.

2009-09-17T12:19:52Z

Added another reference.

← Older revision		Revision as of 14:19, 17 September 2009
Line 1:		Line 1:
	{{Stub-water}}		{{Stub-water}}
	The '''SWM4-DP''' model		The '''SWM4-DP''' model
	<ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water based on classical Drude oscillators", Journal of Chemical Physics '''119''' pp. 5185- (2003)]</ref> of [[water]].		<ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water based on classical Drude oscillators", Journal of Chemical Physics '''119''' pp. 5185- (2003)]</ref>
			<ref>[http://dx.doi.org/10.1063/1.1589749 Guillaume Lamoureux and Benoît Roux "Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm", Journal of Chemical Physics '''119''' pp. 3025- (2003)]</ref>
			of [[water]].
	==SWM4-NDP==		==SWM4-NDP==
	<ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>		<ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>

Nice and Tidy: New page: {{Stub-water}} The '''SWM4-DP''' model [http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water base...

2009-06-26T13:57:50Z

New page: {{Stub-water}} The '''SWM4-DP''' model <ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water base...

New page

{{Stub-water}}
The '''SWM4-DP''' model
<ref>[http://dx.doi.org/10.1063/1.1598191 Guillaume Lamoureux, Alexander D. MacKerell, Jr. and Benoît Roux "A simple polarizable model of water based on classical Drude oscillators", Journal of Chemical Physics '''119''' pp. 5185- (2003)]</ref> of [[water]].
==SWM4-NDP==
<ref>[http://dx.doi.org/10.1016/j.cplett.2005.10.135 Guillaume Lamoureux, Edward Harder, Igor V. Vorobyov, Benoît Roux, and Alexander D. MacKerell Jr. "A polarizable model of water for molecular dynamics simulations of biomolecules", Chemical Physics Letters '''418''' pp. 245-249 (2006)]</ref>
==References==
<references/>
[[category: water]]
[[category: models]]