Ascalaph Designer
ScreenshotImage:DNA-in-Ascalaph-Designer.png
Screenshot altComputer rendering of colored space filling molecular diagram of deoxyribonucleic acid (DNA) made with Ascalaph Designer
AuthorAlexei Nikitin
DeveloperAgile Molecule
Latest release version1.8.94
Latest release date3 December 2015 (age 10)
Programming languageC++
Operating systemWindows
Platformx86
Size138.9 MB
LanguageEnglish
GenreMolecular modelling
LicenseGNU GPL and others including Code Project Open License
Websitewww.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. Vol. 1541. Lecture Notes in Computer Science. Heidelberg: Springer Berlin. pp. 296–303. doi:10.1007/BFb0095310. ISBN 978-3-540-65414-8. S2CID 26892490
  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. S2CID 3358041
  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. ^ "Ascalaph 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. PMID 9936106
  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 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. S2CID 8599984
  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. Comput. Chem.. 28 (12): 2020–2026. doi:10.1002/jcc.20721. PMID 17450554. S2CID 5333395