SWM4-DP model of water: Difference between revisions
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Carl McBride (talk | contribs) (Added a new table for the SWM4-NDP parameters.) |
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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 | | <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. | | 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>. | ||
Revision as of 11:41, 13 January 2014
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The SWM4-DP model [1] [2] of water has a TIP4P like structure, as well as incorporating a Drude oscillator.
Parameters
| (Å) | HOH (deg) | (Å) | (kcal/mol) | q(O) (e) | q(H) (e) | q(M) (e) | (Å) | q(Drude) (e) | k(Drude) (kcal/mol/Å2) |
| 0.9572 | 104.52 | 3.1803 | 0.20568 | -1.77185 | 0.5537 | -2q(H) | 0.23808 | -q(O) | 1000 |
SWM4-NDP
The SWM4-NDP model[3] is a version that has been re-optimized for negatively charged Drude particles. The parameters are given by:
| (Å) | HOH (deg) | (Å) | (kcal/mol) | q(O) (e) | q(H) (e) | q(M) (e) | (Å) | q(Drude) (e) | k(Drude) (kcal/mol/Å2) |
| 0.9572 | 104.52 | 3.18395 | 0.21094 | 1.71636 | 0.55733 | -2q(H) | 0.24034 | -q(O) | 1000 |
SWM6
SWM6 [4].
References
- ↑ 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)
- ↑ 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)
- ↑ 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)
- ↑ 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)