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词条 Ascalaph Designer
释义

  1. Key features

  2. Uses

  3. See also

  4. References

  5. External links

{{Infobox software
| name = Ascalaph Designer
| logo =
| logo alt =
| screenshot = Image:DNA-in-Ascalaph-Designer.png
| caption = Ascalaph Designer renders deoxyribonucleic acid (DNA)
| screenshot alt = Computer rendering of colored space filling molecular diagram of deoxyribonucleic acid (DNA) made with Ascalaph Designer
| collapsible =
| author = Alexei Nikitin
| developer = Agile Molecule
| released =
| discontinued =
| latest release version = 1.8.94
| latest release date = {{Start date and age|2015|12|03|df=yes}}
| latest preview version =
| latest preview date =
| status = Active
| programming language = C++
| operating system = Windows
| platform = x86
| size = 138.9 MB
| language = English
| language count =
| language footnote =
| genre = Molecular modelling
| license = GNU GPL and others including Code Project Open License
| alexa =
| website = {{URL|www.biomolecular-modeling.com/Ascalaph}}
| standard =
| AsOf =
}}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

{{columns-list|colwidth=30em|
  • Molecular model building: polymers, nanotubes, proteins, nucleic acids
  • AMBER-OPLS force field family
  • Geometry optimization
  • Molecular dynamics
  • Quantum chemistry
  • Flexible SPC[7] water model

}}

Uses

{{columns-list|colwidth=30em|
  • Nucleic acids[8]
  • Proteins
  • Modeling lipid bilayers[9]
  • Polyelectrolytes[10]
  • Ionic liquids[11][12]
  • Thermodynamic properties of liquids[13]
  • Chemical force field development[14]

}}

See also

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

References

1. ^{{cite journal |doi= 10.1016/S0010-4655(99)00529-9 |title= MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures | author= A.P.Lyubartsev, A.Laaksonen |journal= Computer Physics Communications |volume= 128 |issue= 3 |year=2000 |pages= 565–589 |bibcode=2000CoPhC.128..565L}}
2. ^{{cite book |title= Applied Parallel Computing Large Scale Scientific and Industrial Problems | chapter= Parallel molecular dynamics simulations of biomolecular systems | author= A.P.Lyubartsev, A.Laaksonen |series= Lecture Notes in Computer Science |publisher= Springer Berlin |location= Heidelberg |volume= 1541 |year=1998 |pages= 296–303 | isbn= 978-3-540-65414-8 |doi= 10.1007/BFb0095310}}
3. ^Computational Chemistry, David Young, Wiley-Interscience, 2001. Appendix A. A.2.3 pg 334, GAMESS
4. ^{{cite journal|title=General Atomic and Molecular Electronic Structure System|year=1993|journal=J. Comput. Chem.|volume=14|issue=11|pages=1347–1363|author=M.W. Schmidt|doi=10.1002/jcc.540141112|display-authors=etal}}
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. ^{{cite journal| doi= 10.1103/PhysRevB.31.2643 | title= Molecular-dynamics study of atomic motions in water |vauthors=Toukan K, Rahman A|lastauthoramp=yes |journal= Physical Review B |volume= 31| issue= 5 |year=1985 |pages= 2643–2648 |bibcode=1985PhRvB..31.2643T}}
8. ^{{cite journal|title= Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study |author1=Y. Cheng, N. Korolev |author2=L. Nordenskiöld |lastauthoramp=yes |journal= Nucleic Acids Research |volume= 34 |year=2006 |pages= 686–696 | pmid= 16449204 | issue= 2 | doi= 10.1093/nar/gkj434 | pmc= 1356527}}
9. ^{{cite journal| title= Modification of the CHARMM force field for DMPC lipid bilayer |author1=C.-J. Högberg |author2=A.M.Nikitin and A.P. Lyubartsev |journal= Journal of Computational Chemistry |volume= 29 |year=2008 |pages= 2359–2369 | pmid= 18512235 | issue= 14 | doi= 10.1002/jcc.20974}}
10. ^{{cite journal| title= Specifics of solvation of sulfonated polyelectrolytes in water, dimethylmethylphosphonate, and their mixture: A molecular simulation study |author1=A. Vishnyakov |author2=A.V. Neimark |lastauthoramp=yes |journal= J. Chem. Phys. |volume= 128 |year=2008 |pages= 164902 | pmid= 18447495 | issue= 16 | doi= 10.1063/1.2899327 |bibcode= 2008JChPh.128p4902V}}
11. ^{{cite journal| title= Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation |author1=G. Raabe |author2=J. Köhler |lastauthoramp=yes |journal= J. Chem. Phys. |volume= 128 |year=2008 |pages= 154509 | pmid= 18433237 | issue= 15 | doi= 10.1063/1.2907332 |bibcode= 2008JChPh.128o4509R}}
12. ^{{cite journal | title= Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF4] and acetonitrile by a refined force field |author1=X. Wu |author2=Z. Liu |author3=S. Huang |author4=W. Wang |journal= Phys. Chem. Chem. Phys. |volume= 7 |year=2005 |pages= 2771–2779 | pmid= 16189592 | issue= 14 | doi= 10.1039/b504681p |bibcode= 2005PCCP....7.2771W}}
13. ^{{cite journal| doi= 10.1039/b108726f | title= Thermodynamic properties and interfacial tension of a model water–carbon dioxide system |author1=T. Kuznetsova |author2=B. Kvamme |lastauthoramp=yes |journal= Phys. Chem. Chem. Phys. |volume= 4| issue= 6 |year=2002 |pages= 937–941 |bibcode= 2002PCCP....4..937K}}
14. ^{{cite journal| doi= 10.1002/jcc.20721 | title= A new six-site acetonitrile model for simulations of liquid acetonitril and its aqueous mixture |author1=A.M. Nikitin |author2=A.P. Lyubartsev |lastauthoramp=yes |journal= J. Comput. Chem. |volume=28 | issue= 12 |year=2007 |pages=2020–2026 | pmid= 17450554 }}

External links

  • {{Official website|www.biomolecular-modeling.com/Ascalaph}}
  • SourceForge
  • [https://twitter.com/agilemolecule Twitter]
{{Chemistry software}}

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