Ascalaph Designer
{{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 =
| 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
| 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{{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}}
.{{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| s2cid= 26892490
}} The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly (formerly named PC GAMESS)Computational Chemistry, David Young, Wiley-Interscience, 2001. Appendix A. A.2.3 pg 334, GAMESS{{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|s2cid=3358041|display-authors=etal}}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. 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).{{Cite web|url=http://sourceforge.net/projects/asc-designer/|title=Ascalaph Designer}}
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{{cite journal
| doi= 10.1103/PhysRevB.31.2643
| title= Molecular-dynamics study of atomic motions in water
|vauthors=Toukan K, Rahman A |journal= Physical Review B |volume= 31
| issue= 5 |year=1985 |pages= 2643–2648 | pmid= 9936106
|bibcode=1985PhRvB..31.2643T
}} water model
}}
Uses
{{columns-list|colwidth=30em|
|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 |name-list-style=amp |journal= Nucleic Acids Research |volume= 34 |year=2006 |pages= 686–696
| pmid= 16449204
| issue= 2
| doi= 10.1093/nar/gkj434
| pmc= 1356527}}
- Proteins
- Modeling lipid bilayers{{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|s2cid=8599984 }}
| title= Specifics of solvation of sulfonated polyelectrolytes in water, dimethylmethylphosphonate, and their mixture: A molecular simulation study
|author1=A. Vishnyakov |author2=A.V. Neimark |name-list-style=amp |journal= J. Chem. Phys. |volume= 128 |year=2008 |pages= 164902
| pmid= 18447495
| issue= 16
| doi= 10.1063/1.2899327 |bibcode= 2008JChPh.128p4902V}}
| title= Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation
|author1=G. Raabe |author2=J. Köhler |name-list-style=amp |journal= J. Chem. Phys. |volume= 128 |year=2008 |pages= 154509
| pmid= 18433237
| issue= 15
| doi= 10.1063/1.2907332 |bibcode= 2008JChPh.128o4509R}}{{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}}
- Thermodynamic properties of liquids{{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 |name-list-style=amp |journal= Phys. Chem. Chem. Phys. |volume= 4
| issue= 6 |year=2002 |pages= 937–941 |bibcode= 2002PCCP....4..937K}}
- Chemical force field development{{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 |name-list-style=amp |journal= J. Comput. Chem. |volume=28
| issue= 12 |year=2007 |pages=2020–2026
| pmid= 17450554
| s2cid= 5333395
}}
}}
See also
References
{{Reflist}}
External links
- {{Official website|www.biomolecular-modeling.com/Ascalaph}}
- [http://sourceforge.net/projects/asc-designer SourceForge]
- [https://twitter.com/agilemolecule Twitter]
{{Chemistry software}}
Category:Computational chemistry software
Category:Free science software