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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; 9 years ago (2015-12-03)
Written in	C++
Operating system	Windows
Platform	x86
Size	138.9 MB
Available in	English
Type	Molecular modelling
License	GNU GPL and others including Code Project Open License
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 . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly (formerly named PC GAMESS) 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).

Key features

• Molecular model building: polymers, nanotubes, proteins, nucleic acids
• AMBER-OPLS force field family
• Geometry optimization
• Molecular dynamics
• Quantum chemistry
• Flexible SPC water model

Uses

• Nucleic acids
• Proteins
• Modeling lipid bilayers
• Polyelectrolytes
• Ionic liquids
• Thermodynamic properties of liquids
• Chemical force field development

See also

• List of software for molecular mechanics modeling
• Molecular design software
• Molecule editor
• Abalone

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. Vol. 1541. 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 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.

External links

• Official website
• SourceForge
• Twitter

• Computational chemistry software
• Free science software
• Molecular modelling software
• Molecular dynamics software