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Ascalaph Designer


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


  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.  
  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.  
  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.  
  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. ^
  7. ^ Toukan K and Rahman A (1985). "Molecular-dynamics study of atomic motions in water". Physical Review B 31 (5): 2643–2648.  
  8. ^ Y. Cheng, N. Korolev and L. Nordenskiöld (2006). with condensed ordered DNA. A molecular dynamics computer simulation study"+ and Na+"Similarities and differences in interaction of K. Nucleic Acids Research 34 (2): 686–696.  
  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.  
  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.  
  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.  
  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.  
  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.  
  14. ^ A.M. Nikitin and A.P. Lyubartsev (2007). "A new six-site  

External links

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