Stochastic dynamics simulation of alanine dipeptide: Including solvation interaction determined by boundary element method
✍ Scribed by Wan, Shun Zhou; Wang, Cun Xin; Xiang, Zhe Xin; Shi, Yun Yu
- Publisher
- John Wiley and Sons
- Year
- 1997
- Tongue
- English
- Weight
- 226 KB
- Volume
- 18
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
A merger of the Poisson᎐Boltzmann equation and stochastic dynamics simulation is examined using illustrative calculations of alanine Ž . dipeptide. The boundary element method BEM is used to calculate the hydration forces acting on the solute molecule based on the surroundings. Computational efficiency is achieved by the use of a simple hydration model and a coarse boundary element. Nonetheless, the conformational distribution obtained from this new method is reasonable compared with other theoretical and computational results. Detailed analysis has been accomplished in terms of the hydration interactions and solvation energies. The results indicate that the new simulation method provides an obvious improvement over the conventional stochastic dynamics simulation technique. The further improvement of the hydration model and future application to large molecules are also discussed.