SWM4-DP model of water: Difference between revisions
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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> | ||
Latest revision as of 11:14, 13 January 2014
The SWM4-DP model [1] [2] of water has a TIP4P like structure, as well as incorporating a Drude oscillator.
Parameters[edit]
| (Å) | HOH (deg) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \sigma} (Å) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \epsilon} (kcal/mol) | q(O) (e) | q(H) (e) | q(M) (e) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle r_{\mathrm {OM}}} (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[edit]
The SWM4-NDP model[3] is a version that has been re-optimized for negatively charged Drude particles. The parameters are given by:
| Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle r_{\mathrm {OH}}} (Å) | HOH (deg) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \sigma} (Å) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \epsilon} (kcal/mol) | q(O) (e) | q(H) (e) | q(M) (e) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle r_{\mathrm {OM}}} (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[edit]
The SWM6 [4] model is a six-site model that adds oxygen lone-pairs (Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle L} ) to the SWM4-NDP model. The parameters are given by:
| (Å) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \angle} HOH (deg) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \angle} LOL (deg) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle R_{ \mathrm{min, O} }} (Å) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \epsilon} (kcal/mol) | q(O) (e) | q(H) (e) | q(M) (e) | q(L) (e) | (Å) | Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle r_{\mathrm {OL}}} (Å) | q(Drude) (e) | k(Drude) (kcal/mol/Å2) |
| 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[edit]
- ↑ 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)