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497:, and Langevin). The code also supports methods for restraining atomic positions and molecular configurations; allows simulations to be carried out using a variety of periodic cell configurations; and has facilities for accurate checkpointing and restart.
594:
Bowers, Kevin J.; Chow, Edmond; Xu, Huafeng; Dror, Ron O.; Eastwood, Michael P.; Gregersen, Brent A.; Klepeis, John L.; Kolossvary, Istvan; Moraes, Mark A.; Sacerdoti, Federico D.; Salmon, John K.; Shan, Yibing; Shaw, David E. (2006).
527:
Along with the molecular dynamics program, the
Desmond software also includes tools for minimizing and energy analysis, both of which can be run efficiently in a parallel environment.
432:. The code uses novel parallel algorithms and numerical methods to achieve high performance on platforms containing multiple processors, but may also be executed on a single computer.
494:
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1011:
Shan, Yibing; Klepeis, John L.; Eastwood, Michael P.; Dror, Ron O.; Shaw, David E. (2005). "Gaussian split Ewald: A fast Ewald mesh method for molecular simulation".
554:
574:
458:
Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using
932:
Edmond Chow; Charles A. Rendleman; Kevin J. Bowers; Ron O. Dror; Douglas H. Hughes; Justin
Gullingsrud; Federico D. Sacerdoti; David E. Shaw (July 2008).
875:
Lippert, Ross A.; Bowers, Kevin J.; Dror, Ron O.; Eastwood, Michael P.; Gregersen, Brent A.; Klepeis, John L.; Kolossvary, Istvan; Shaw, David E. (2007).
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formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (
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are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the
710:"Identification of two distinct inactive conformations of the 2-adrenergic receptor reconciles structural and biochemical observations"
508:) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.
596:
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649:
Jensen, M. O.; Borhani, D. W.; Lindorff-Larsen, K.; Maragakis, P.; Jogini, V.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. (2010).
245:
1062:
Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L.; Dror, Ron O.; Shaw, David E. (2010).
144:
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Shan, Y.; Seeliger, M. A.; Eastwood, M. P.; Frank, F.; Xu, H.; Jensen, M. O.; Dror, R. O.; Kuriyan, J.; Shaw, D. E. (2009).
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Bowers, K.J.; Lippert, R.A.; Dror, R.O.; Shaw, D.E. (2010). "Improved
Twiddle Access for Fast Fourier Transforms".
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algorithm. These methods can be used together with time-scale splitting (RESPA-based) integration schemes.
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used in biomolecular simulations, and is also compatible with polarizable force fields based on the
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Force fields parameters can be assigned using a template-based parameter assignment tool called
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Desmond can also be used to perform absolute and relative free energy calculations (e.g.,
8:
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Dror, R. O.; Arlow, D. H.; Borhani, D. W.; Jensen, M. O.; Piana, S.; Shaw, D. E. (2009).
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561:) for setting up simulations of biological and chemical systems, and is compatible with
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769:"A conserved protonation-dependent switch controls drug binding in the Abl kinase"
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1064:"Improved side-chain torsion potentials for the Amber ff99SB protein force field"
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It may require cleanup to comply with
Knowledge's content policies, particularly
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597:"Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters"
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Desmond can compute energies and forces for many standard fixed-charged
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877:"A common, avoidable source of error in molecular dynamics integrators"
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515:(GPU) accelerated version that is about 60-80 times faster than the
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Desmond is integrated with a molecular modeling environment (
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List of quantum chemistry and solid-state physics software
936:. D. E. Shaw Research Technical Report DESRES/TR--2008-01.
934:"Desmond Performance on a Cluster of Multicore Processors"
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Bowers, Kevin J.; Dror, Ron O.; Shaw, David E. (2006).
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Comparison of software for molecular mechanics modeling
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distributed computing project. Desmond is available as
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462:-based methods. Constraints can be enforced using the
74:
A major contributor to this article appears to have a
967:
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428:simulations of biological systems on conventional
1068:Proteins: Structure, Function, and Bioinformatics
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534:. It currently supports several versions of the
773:Proceedings of the National Academy of Sciences
714:Proceedings of the National Academy of Sciences
655:Proceedings of the National Academy of Sciences
825:
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565:(VMD) for trajectory viewing and analysis.
53:Learn how and when to remove these messages
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283:Learn how and when to remove this message
265:Learn how and when to remove this message
105:Learn how and when to remove this message
1559:List of protein-ligand docking software
546:force fields, and a range of different
2211:
970:IEEE Transactions on Signal Processing
201:Please improve this article by adding
1158:
504:). Other simulation methods (such as
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18:
16:Software for computational chemistry
604:ACM/IEEE SC 2006 Conference (SC'06)
420:is a software package developed at
13:
1384:List of molecular graphics systems
14:
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34:This article has multiple issues.
1150:Schrödinger Desmond Product Page
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85:. Please discuss further on the
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23:
1618:Molecular Operating Environment
1519:Molecular Operating Environment
1104:
1055:
1013:The Journal of Chemical Physics
881:The Journal of Chemical Physics
832:The Journal of Chemical Physics
511:Desmond is also available in a
42:or discuss these issues on the
1211:Avalon Cheminformatics Toolkit
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502:free energy perturbation
489:) and pressure control (
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1112:"DEShawResearch/Viparr"
794:10.1073/pnas.0811223106
735:10.1073/pnas.0811065106
676:10.1073/pnas.0911691107
517:central processing unit
359:Computational chemistry
214:"Desmond" software
949:Cite journal requires
523:Related software tools
424:to perform high-speed
190:relies excessively on
83:neutral point of view
495:Martyna-Tobias-Klein
152:improve this article
2123:JME Molecule Editor
1372:Molecular modelling
1144:Desmond Users Group
1025:2005JChPh.122e4101S
982:2010ITSP...58.1122B
893:2007JChPh.126d6101L
844:2006JChPh.124r4109B
785:2009PNAS..106..139S
726:2009PNAS..106.4689D
667:2010PNAS..107.5833J
479:Andersen thermostat
460:particle mesh Ewald
445:commercial software
422:D. E. Shaw Research
378:commercial software
307:D. E. Shaw Research
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156:independent sources
2058:Skeletal structure
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426:molecular dynamics
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902:10.1063/1.2431176
853:10.1063/1.2191489
720:(12): 4689–4694.
661:(13): 5833–5838.
621:978-0-7695-2700-0
559:Schrödinger, Inc.
449:Schrödinger, Inc.
430:computer clusters
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2128:MarvinSketch
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1534:UCSF Chimera
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1220:Blue Obelisk
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633:. Retrieved
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471:force fields
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441:Folding@home
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345:Available in
302:Developer(s)
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164:October 2013
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150:Please help
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95:October 2013
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36:Please help
33:
2105:BIOVIA Draw
2093:Proprietary
1954:GAMESS (US)
1949:GAMESS (UK)
1892:Proprietary
1679:Proprietary
1600:Proprietary
1457:Proprietary
1326:Proprietary
1273:Chemicalize
1260:Proprietary
483:Nosé-Hoover
437:source code
405:schrodinger
371:Proprietary
141:and may be
132:reads like
2213:Categories
2118:ChemWindow
2109:ChemDoodle
2074:JChemPaint
1883:YAMBO code
1837:OpenMolcas
1509:MarvinView
1484:ChemWindow
1245:Open Babel
635:2009-01-16
581:References
395:/resources
225:newspapers
192:references
39:improve it
2195:OpenChrom
2084:XDrawChem
2079:Molsketch
2029:TURBOMOLE
2009:Quantemol
1215:Bioclipse
1146:(deleted)
491:Berendsen
87:talk page
45:talk page
2158:EXC code
2113:ChemDraw
2024:TeraChem
2014:Scigress
1984:OpenAtom
1959:Gaussian
1852:PyQuante
1777:CONQUEST
1772:COLUMBUS
1575:AutoDock
1514:MODELLER
1494:Gaussian
1479:ChemDraw
1423:Ghemical
1403:Avogadro
1333:Autochem
1188:software
1098:20408171
1049:35865319
1041:15740304
998:17240443
919:38661350
911:17286520
862:16709099
813:19109437
754:19258456
695:20231479
569:See also
487:Langevin
447:through
409:/desmond
397:_desmond
374:freeware
326:Platform
154:and add
2199:SASHIMI
2169:Mercury
2060:drawing
2019:Spartan
1944:Firefly
1939:CRYSTAL
1864:(PWscf)
1832:Octopus
1812:MADNESS
1797:DP code
1758:(CFOUR)
1707:Desmond
1687:Abalone
1654:GROMACS
1585:FlexAID
1529:Spartan
1499:Maestro
1464:Abalone
1443:QuteMol
1433:Molekel
1418:Gabedit
1358:Khimera
1348:COSILAB
1343:CHEMKIN
1312:Cantera
1089:2970904
1021:Bibcode
978:Bibcode
889:Bibcode
840:Bibcode
804:2610013
781:Bibcode
745:2650503
722:Bibcode
686:2851896
663:Bibcode
555:Maestro
464:M-SHAKE
418:Desmond
384:Website
366:License
348:English
296:Desmond
239:scholar
2190:Molden
2141:Others
2039:WIEN2k
2004:Q-Chem
1979:ONETEP
1974:MOLPRO
1969:MOLCAS
1964:Jaguar
1934:CRUNCH
1924:CASTEP
1919:CASINO
1914:CADPAC
1878:VB2000
1873:SIESTA
1842:PARSEC
1827:NWChem
1807:FreeON
1787:Dalton
1767:BigDFT
1762:AIMAll
1751:ABINIT
1712:GROMOS
1697:CHARMM
1669:PLUMED
1664:OpenMM
1659:LAMMPS
1613:LeDock
1524:SAMSON
1448:RasMol
1413:Biskit
1353:DelPhi
1268:Canvas
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1994:PLATO
1909:DMol3
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1802:FLEUR
1792:DIRAC
1692:AMBER
1608:Glide
1590:rDock
1489:EzMol
1438:PyMOL
1250:RDKit
1240:OELib
1045:S2CID
994:S2CID
915:S2CID
629:(PDF)
600:(PDF)
540:Amber
475:Drude
399:.html
319:Linux
246:JSTOR
232:books
2165:GSim
2162:GenX
2044:XMVB
2034:VASP
1989:ORCA
1929:CPMD
1822:MPQC
1782:CP2K
1756:ACES
1717:NAMD
1702:CPMD
1649:CP2K
1428:Jmol
1408:BALL
1375:and
1307:APBS
1230:ECCE
1094:PMID
1037:PMID
955:help
907:PMID
858:PMID
809:PMID
750:PMID
691:PMID
616:ISBN
544:OPLS
542:and
407:.com
393:.com
354:Type
218:news
2179:ICM
1999:PQS
1899:ADF
1868:RMG
1847:PSI
1539:VMD
1317:KPP
1084:PMC
1076:doi
1029:doi
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799:PMC
789:doi
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740:PMC
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389:www
331:x86
194:to
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