Модель ДНК на Ascalaph Designer
Ascalaph Designer — программа молекулярного моделирования общего назначения. Она предоставляет графическое окружение для консольных программ квантовой и классической механики Firefly, CP2K и MDynaMix[1] [2], имеет возможности для конструирования молекулярных моделей, конформационной оптимизации и молекулярной динамики. Firefly/PC GAMESS[3][4][5] предоставляет широкий ряд квантовохимических методов.
Основные возможности
Область применения
Примечания
- ↑ A.P.Lyubartsev, A.Laaksonen (2000). «MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures». Computer Physics Communications 128: 565–589.
- ↑ A.P.Lyubartsev, A.Laaksonen Parallel molecular dynamics simulations of biomolecular systems // Applied Parallel Computing Large Scale Scientific and Industrial Problems. — Heidelberg: Springer Berlin, 1998. — Vol. 1541. — P. 296–303. — ISBN 978-3-540-65414-8
- ↑ Computational Chemistry, David Young, Wiley-Interscience, 2001. Appendix A. A.2.3 pg 334, GAMESS
- 10.1002/jcc.540141112.
- ↑ M. S. Gordon and M. W. Schmidt, Advances in electronic structure theory: GAMESS a decade later, in Theory and Applications of Computational Chemistry, the first 40 years, C. E. Dykstra, G. Frenking. K. S. Lim and G. E. Scusaria, Elsevier, Amsterdam, 2005.
- ↑ Toukan K and Rahman A (1985). «Molecular-dynamics study of atomic motions in water». Physical Review B 31: 2643–2648.
- ↑ Y. Cheng, N. Korolev and L. Nordenskiöld (2006). «Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study». Nucleic Acids Research 34: 686–696.
- ↑ C.-J. Högberg, A.M.Nikitin and A.P. Lyubartsev (2008). «Modification of the CHARMM force field for DMPC lipid bilayer». Journal of Computational Chemistry 29: 2359–2369.
- ↑ A. Vishnyakov and A.V. Neimark (2008). «Specifics of solvation of sulfonated polyelectrolytes in water, dimethylmethylphosphonate, and their mixture: A molecular simulation study». J. Chem. Phys. 128: 164902.
- ↑ G. Raabe and J. Köhler (2008). «Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation». J. Chem. Phys. 128: 154509.
- ↑ X. Wu, Z. Liu, S. Huang and W. Wang (2005). «Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF4] and acetonitrile by a refined force field». Phys. Chem. Chem. Phys. 7: 2771–2779.
- ↑ T. Kuznetsova and B. Kvamme (2002). «Thermodynamic properties and interfacial tension of a model water–carbon dioxide system». Phys. Chem. Chem. Phys. 4: 937–941.
- ↑ A.M. Nikitin and A.P. Lyubartsev (2007). «A new six-site acetonitrile model for simulations of liquid acetonitril and its aqueous mixture». J. Comp. Chem. 28: 2020–2026.
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