AMBER forcefield: Difference between revisions
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==Force field== | |||
<math>E_{\rm total} = \sum_{\rm bonds} K_r (r - r_{eq})^2 | |||
+ \sum_{\rm angles} K_\theta (\theta - \theta_{eq})^2 | |||
+ \sum_{\rm dihedrals} {V_n \over 2} | |||
[1 + {\rm cos}(n\phi - \gamma)] | |||
+ \sum_{i<j} \left [ {A_{ij} \over R_{ij}^{12}} - | |||
{B_{ij} \over R_{ij}^6} + | |||
{q_iq_j \over \epsilon R_{ij}} | |||
\right ] | |||
+ \sum_{\rm H-bonds} | |||
\left [ {C_{ij} \over R_{ij}^{12}} - | |||
{D_{ij} \over R_{ij}^{10}} \right ] </math> | |||
==External links== | ==External links== | ||
*[http://amber.scripps.edu/dbase.html AMBER parameters] | |||
*[http://amber.scripps.edu/dbase.html | |||
==References== | ==References== | ||
#[http://dx.doi.org/10.1021/ja00124a002 Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, and Peter A. Kollman "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", Journal of the American Chemical Society '''117''' pp 5179 - 5197 (1995)] | |||
#[http://dx.doi.org/10.1016/0010-4655(95)00041-D David A. Pearlman, David A. Case, James W. Caldwell, Wilson S. Ross, Thomas E. Cheatham, Steve DeBolt, David Ferguson, George Seibel and Peter Kollman "AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules", Computer Physics Communications '''91''' pp. 1-41 (1995)] | #[http://dx.doi.org/10.1016/0010-4655(95)00041-D David A. Pearlman, David A. Case, James W. Caldwell, Wilson S. Ross, Thomas E. Cheatham, Steve DeBolt, David Ferguson, George Seibel and Peter Kollman "AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules", Computer Physics Communications '''91''' pp. 1-41 (1995)] | ||
[[category:Force fields]] | [[category:Force fields]] | ||
Revision as of 15:58, 6 November 2007
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Force field
![{\displaystyle E_{\rm {total}}=\sum _{\rm {bonds}}K_{r}(r-r_{eq})^{2}+\sum _{\rm {angles}}K_{\theta }(\theta -\theta _{eq})^{2}+\sum _{\rm {dihedrals}}{V_{n} \over 2}[1+{\rm {cos}}(n\phi -\gamma )]+\sum _{i<j}\left[{A_{ij} \over R_{ij}^{12}}-{B_{ij} \over R_{ij}^{6}}+{q_{i}q_{j} \over \epsilon R_{ij}}\right]+\sum _{\rm {H-bonds}}\left[{C_{ij} \over R_{ij}^{12}}-{D_{ij} \over R_{ij}^{10}}\right]}](https://wikimedia.org/api/rest_v1/media/math/render/svg/07abb3f2d6f16ca1e1dede075b6faf02bc42b5df)
External links
References
- Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, and Peter A. Kollman "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules", Journal of the American Chemical Society 117 pp 5179 - 5197 (1995)
- David A. Pearlman, David A. Case, James W. Caldwell, Wilson S. Ross, Thomas E. Cheatham, Steve DeBolt, David Ferguson, George Seibel and Peter Kollman "AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules", Computer Physics Communications 91 pp. 1-41 (1995)