Ascalaph Designer

DNA on Ascalaph Designer

Ascalaph Designer is a general purpose molecular modelling package for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix[1] .[2] The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. The Firefly/PC GAMESS[3][4][5] covers a wide range of quantum chemistry methods. Ascalaph Designer is released under the GNU GPL.[6]

Key features

Field of application

See also

References

  1. ↑ A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications 128 (3): 565–589. Bibcode:2000CoPhC.128..565L. doi:10.1016/S0010-4655(99)00529-9.
  2. ↑ A.P.Lyubartsev, A.Laaksonen (1998). "Parallel molecular dynamics simulations of biomolecular systems". Applied Parallel Computing Large Scale Scientific and Industrial Problems. Lecture Notes in Computer Science 1541. Heidelberg: Springer Berlin. pp. 296–303. doi:10.1007/BFb0095310. ISBN 978-3-540-65414-8.
  3. ↑ Computational Chemistry, David Young, Wiley-Interscience, 2001. Appendix A. A.2.3 pg 334, GAMESS
  4. ↑ M.W. Schmidt; et al. (1993). "General Atomic and Molecular Electronic Structure System". J. Comput. Chem. 14 (11): 1347–1363. doi:10.1002/jcc.540141112.
  5. ↑ 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.
  6. ↑ http://sourceforge.net/projects/asc-designer/
  7. ↑ Toukan K and Rahman A (1985). "Molecular-dynamics study of atomic motions in water". Physical Review B 31 (5): 2643–2648. Bibcode:1985PhRvB..31.2643T. doi:10.1103/PhysRevB.31.2643.
  8. ↑ 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 (2): 686–696. doi:10.1093/nar/gkj434. PMC 1356527. PMID 16449204.
  9. ↑ 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 (14): 2359–2369. doi:10.1002/jcc.20974. PMID 18512235.
  10. ↑ 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 (16): 164902. Bibcode:2008JChPh.128p4902V. doi:10.1063/1.2899327. PMID 18447495.
  11. ↑ G. Raabe and J. Köhler (2008). "Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation". J. Chem. Phys. 128 (15): 154509. Bibcode:2008JChPh.128o4509R. doi:10.1063/1.2907332. PMID 18433237.
  12. ↑ 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 (14): 2771–2779. Bibcode:2005PCCP....7.2771W. doi:10.1039/b504681p. PMID 16189592.
  13. ↑ T. Kuznetsova and B. Kvamme (2002). "Thermodynamic properties and interfacial tension of a model water–carbon dioxide system". Phys. Chem. Chem. Phys. 4 (6): 937–941. Bibcode:2002PCCP....4..937K. doi:10.1039/b108726f.
  14. ↑ 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 (12): 2020–2026. doi:10.1002/jcc.20721. PMID 17450554.

External links

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