SklogWiki - User contributions [en]

Talk:SWM4-DP model of water

2014-01-13T02:18:17Z

24.168.13.79: Created page with "Sorry, I don't have an account here but I edited the page because it seems there were errors on the charges. I took the SWM4-NDP parameters straight from the Drude_Oct_13 CHA..."

Sorry, I don't have an account here but I edited the page because it seems there were errors on the charges. I took the SWM4-NDP parameters straight from the Drude_Oct_13 CHARMM .tar.gz file and updated the oxygen OM LP charge and the epsilon on the ODW oxygen (there seems to be no VDW parameters on the hydrogens). The sigma I calculated was 3.1828082 Å seems close enough so I left it as-is. -Luke Czapla

SWM4-DP model of water

2014-01-13T02:14:16Z

24.168.13.79: /* Parameters */

{{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>
<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]] 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 || 0.210943 || -1.11466 || 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>.
==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/>
[[category: water]]
[[category: models]]

SWM4-DP model of water

2014-01-13T02:12:03Z

24.168.13.79: /* Parameters */

{{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>
<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]] 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 || -1.11466 || 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>.
==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/>
[[category: water]]
[[category: models]]