Ascalaph Designer

Ascalaph Designer

Computer rendering of colored space filling molecular diagram of deoxyribonucleic acid (DNA) made with Ascalaph Designer

Ascalaph Designer renders deoxyribonucleic acid (DNA)
Original author(s) Alexei Nikitin
Developer(s) Agile Molecule
Stable release
1.8.94 / 3 December 2015 (2015-12-03)
Development status Active
Written in C++
Operating system Windows, Linux
Platform x86
Size 138.9 MB
Available in English
Type Molecular modelling
License GPLv2
Website www.biomolecular-modeling.com/Ascalaph

Ascalaph Designer is a computer program for general purpose molecular modelling 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. Firefly (formerly named PC GAMESS)[3][4][5] covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2).[6]

Key features

Uses

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 & 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 & 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 1356527Freely accessible. 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 & 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 & 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; 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 & 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 & 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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