Ascalaph Designer

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]

Original authorAlexei Nikitin

DeveloperAgile Molecule

Stable release

1.8.94 / 3 December 2015; 10 years ago

Written inC++

Quick facts Original author, Developer ...

Ascalaph Designer
Ascalaph Designer renders deoxyribonucleic acid (DNA)
Original author	Alexei Nikitin
Developer	Agile Molecule

Stable release	1.8.94 / 3 December 2015; 10 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

Key features

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

Nucleic acids^[8]
Proteins
Modeling lipid bilayers^[9]
Polyelectrolytes^[10]
Ionic liquids^[11]^[12]
Thermodynamic properties of liquids^[13]
Chemical force field development^[14]

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 [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.

Ascalaph Designer

Key features

Uses

See also

References

External links

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