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{{Short description|Software for computational chemistry}}
'''Desmond''' is a software package developed at [[D. E. Shaw Research]] to perform high-speed [[molecular dynamics]] simulations of biological systems on conventional computer clusters.<ref>{{cite journal|
{{multiple issues|
publisher=[[Association for Computing Machinery|ACM]]|
{{COI|date=October 2013}}
author=Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw|
{{news release|date=October 2013}}
title=Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters|
{{Primary sources|date=November 2019}}
url=http://sc06.supercomputing.org/schedule/pdf/pap259.pdf|
}}
isbn=0-7695-2700-0|
{{Infobox software
journal=Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006.|
|name = Desmond
year=2006
|developer = [[D. E. Shaw Research]]
}}</ref><ref>{{cite journal|
|operating system = [[Linux]]
publisher=[[PNAS]]|
|platform = [[x86]], [[x86-64]], [[computer cluster]]s
author=Morten Ø. Jensen, David W. Borhani, Kresten Lindorff-Larsen, Paul Maragakis, Vishwanath Jogini, Michael P. Eastwood, Ron O. Dror, and David E. Shaw|
|size =
title=Principles of Conduction and Hydrophobic Gating in K+ Channels|
|language = English
url=http://www.pnas.org/content/107/13/5833.full|
|genre = [[Computational chemistry]]
journal=Proceedings of the National Academy of Sciences of the United States of America|
|license = [[Proprietary software|Proprietary]] [[freeware]], [[commercial software]]
volume= 107|
|website = {{URL|www.deshawresearch.com/resources_desmond.html}}, {{URL|schrodinger.com/desmond}}
pages= 5833–5838|
}}
doi=10.1073/pnas.0911691107|
'''Desmond''' is a software package developed at [[D. E. Shaw Research]] to perform high-speed [[molecular dynamics]] simulations of biological systems on conventional [[computer cluster]]s.<ref>{{cite book
year=2010|
|chapter-url=http://sc06.supercomputing.org/schedule/pdf/pap259.pdf
pmid=20231479|
|doi=10.1109/SC.2006.54
issue=13|
|isbn=978-0-7695-2700-0
pmc=2851896
|chapter=Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
}}</ref><ref>{{cite journal|
|title=ACM/IEEE SC 2006 Conference (SC'06)
publisher=[[PNAS]]|
|pages=43
author=Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, and David E. Shaw|
|year=2006
title=Identification of Two Distinct Inactive Conformations of the ß2-Adrenergic Receptor Reconciles Structural and Biochemical Observations|
|last1=Bowers
url=http://www.pnas.org/content/106/12/4689.full|
|first1=Kevin J.
doi=10.1073/pnas.0811065106|
|last2=Chow
journal=Proceedings of the National Academy of Sciences of the United States of America|
|first2=Edmond
volume= 106|
|last3=Xu
pages= 4689–4694|
|first3=Huafeng
year=2009|
|last4=Dror
pmid=19258456|
|first4=Ron O.
issue=12|
|last5=Eastwood
pmc=2650503
|first5=Michael P.
}}</ref><ref>{{cite journal|
|last6=Gregersen
publisher=[[PNAS]]|
|first6=Brent A.
author=Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, Filipp Frank, Huafeng Xu, Morten Ø. Jensen, Ron O. Dror, John Kuriyan, and David E. Shaw|
|last7=Klepeis
title=A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase|
|first7=John L.
url=http://www.pnas.org/content/106/1/139.full|
|last8=Kolossvary
doi=10.1073/pnas.0811223106|
|first8=Istvan
journal=Proceedings of the National Academy of Sciences of the United States of America|
|last9=Moraes
volume=106|
|first9=Mark A.
pages=139–144|
|last10=Sacerdoti
year=2009|
|first10=Federico D.
pmid=19109437|
|last11=Salmon
issue=1|
|first11=John K.
pmc=2610013
|last12=Shan
}}</ref> The code uses novel parallel algorithms<ref>{{cite journal|
|first12=Yibing
publisher=[[J. Chem. Phys.]]|
|last13=Shaw
author=Kevin J. Bowers, Ron O. Dror, and David E. Shaw|
|first13=David E.
title=The Midpoint Method for Parallelization of Particle Simulations|
|access-date=2009-01-16
url=http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000124000018184109000001&idtype=cvips&gifs=yes|
|archive-date=2008-08-28
doi=10.1063/1.2191489|
|archive-url=https://web.archive.org/web/20080828224042/http://sc06.supercomputing.org/schedule/pdf/pap259.pdf
journal=Journal of Chemical Physics|
|url-status=dead
volume=124|
}}</ref><ref>
pages=184109:1–11|
{{cite journal
year=2006|
|bibcode=2010PNAS..107.5833J
pmid=16709099|
|doi=10.1073/pnas.0911691107
issue=18
|pmc=2851896
}}</ref> and numerical techniques<ref>{{cite journal|
|pmid=20231479
publisher=[[J. Chem. Phys.]]|
|title=Principles of conduction and hydrophobic gating in K+ channels
author=Ross A. Lippert, Kevin J. Bowers, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, and David E. Shaw|
|journal=Proceedings of the National Academy of Sciences
title=A Common, Avoidable Source of Error in Molecular Dynamics Integrators|
|volume=107 |issue=13 |pages=5833–5838
url=http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000126000004046101000001&idtype=cvips&gifs=yes|
|year=2010
doi=10.1063/1.2431176|
|last1=Jensen |first1=M. O.
journal=Journal of Chemical Physics|
|last2=Borhani |first2=D. W.
volume=126|
|last3=Lindorff-Larsen |first3=K.
pages=046101:1–2|
|last4=Maragakis |first4=P.
year=2007|
|last5=Jogini |first5=V.
pmid=17286520|
|last6=Eastwood |first6=M. P.
issue=4
|last7=Dror |first7=R. O.
}}</ref> to achieve high performance on platforms containing a large number of processors,<ref>{{cite journal|
|last8=Shaw |first8=D. E.
author=Edmond Chow, Charles A. Rendleman, Kevin J. Bowers, Ron O. Dror, Douglas H. Hughes, Justin Gullingsrud, Federico D. Sacerdoti, and David E. Shaw|
|doi-access=free
title=Desmond Performance on a Cluster of Multicore Processors|
}}</ref><ref>
url=http://deshawresearch.com/publications.html|
{{cite journal
publisher=D. E. Shaw Research Technical Report DESRES/TR--2008-01, July 2008|
|doi=10.1073/pnas.0811065106
year=2008}}</ref> but may also be executed on a single computer. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions. Desmond is available for commercial use through [[Schrödinger (company)|Schrödinger]].
|pmid=19258456
|pmc=2650503
|title=Identification of two distinct inactive conformations of the 2-adrenergic receptor reconciles structural and biochemical observations
|journal=Proceedings of the National Academy of Sciences
|volume=106 |issue=12 |pages=4689–4694
|year=2009
|last1=Dror |first1=R. O.
|last2=Arlow |first2=D. H.
|last3=Borhani |first3=D. W.
|last4=Jensen |first4=M. O.
|last5=Piana |first5=S.
|last6=Shaw |first6=D. E. |bibcode=2009PNAS..106.4689D
|doi-access=free
}}</ref><ref>
{{cite journal
|bibcode=2009PNAS..106..139S
|doi=10.1073/pnas.0811223106
|pmc=2610013
|pmid=19109437
|title=A conserved protonation-dependent switch controls drug binding in the Abl kinase
|journal=Proceedings of the National Academy of Sciences
|volume=106 |issue=1 |pages=139–144
|year=2009
|last1=Shan |first1=Y.
|last2=Seeliger |first2=M. A.
|last3=Eastwood |first3=M. P.
|last4=Frank |first4=F.
|last5=Xu |first5=H.
|last6=Jensen |first6=M. O.
|last7=Dror |first7=R. O.
|last8=Kuriyan |first8=J.
|last9=Shaw |first9=D. E.
|doi-access=free
}}</ref> The code uses novel parallel algorithms<ref>
{{cite journal
|doi=10.1063/1.2191489
|pmid=16709099
|bibcode=2006JChPh.124r4109B
|title=The midpoint method for parallelization of particle simulations
|journal=The Journal of Chemical Physics
|volume=124 |issue=18 |pages=184109
|year=2006
|last1=Bowers |first1=Kevin J.
|last2=Dror |first2=Ron O.
|last3=Shaw |first3=David E.
|doi-access=free
}}</ref> and numerical methods<ref>
{{cite journal
|doi=10.1063/1.2431176
|pmid=17286520
|bibcode=2007JChPh.126d6101L
|title=A common, avoidable source of error in molecular dynamics integrators
|journal=The Journal of Chemical Physics
|volume=126 |issue=4 |pages=046101
|year=2007
|last1=Lippert |first1=Ross A.
|last2=Bowers |first2=Kevin J.
|last3=Dror |first3=Ron O.
|last4=Eastwood |first4=Michael P.
|last5=Gregersen |first5=Brent A.
|last6=Klepeis |first6=John L.
|last7=Kolossvary |first7=Istvan
|last8=Shaw |first8=David E.
|s2cid=38661350
|doi-access=free
}}</ref> to achieve high performance on platforms containing multiple processors,<ref>
{{cite journal
|author1=Edmond Chow
|author2=Charles A. Rendleman
|author3=Kevin J. Bowers
|author4=Ron O. Dror
|author5=Douglas H. Hughes
|author6=Justin Gullingsrud
|author7=Federico D. Sacerdoti
|author8=David E. Shaw
|date=July 2008
|title=Desmond Performance on a Cluster of Multicore Processors
|url=http://deshawresearch.com/publications.html
|publisher=D. E. Shaw Research Technical Report DESRES/TR--2008-01
}}</ref> but may also be executed on a single computer.


The core and [[source code]] are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the [[Folding@home]] distributed computing project. Desmond is available as [[commercial software]] through [[Schrödinger (company)|Schrödinger, Inc.]]
== Desmond molecular dynamics program ==


==Molecular dynamics program==
Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using [[Ewald_summation#Particle_mesh_Ewald_.28PME.29_method|particle-mesh-based Ewald]] techniques.<ref>{{cite journal|
publisher=[[IEEE]]|
author=Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, and David E. Shaw|
title=Improved Twiddle Access for Fast Fourier Transforms|
url=http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5313934&tag=1|
doi=10.1109/TSP.2009.2035984 |
journal=IEEE Transactions on Signal Processing|
volume=58|
issue=3|
pages=1122–1130|
year=2010
}}</ref><ref>{{cite journal|
publisher=[[J. Chem. Phys.]]|
author=Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror and David E. Shaw|
title=Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation|
url=http://jcp.aip.org/jcpsa6/v122/i5/p054101_s1|
doi=10.1063/1.1839571|
journal=Journal of Chemical Physics|
volume=122|
pages=054101:1–13|
year=2005|
pmid=15740304|
issue=5
}}</ref> Constraints can be enforced using the [[M-SHAKE#The_M-SHAKE_algorithm|M-SHAKE]] algorithm. These approaches can be used in combination with time-scale splitting (RESPA-based) integration schemes.


Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using [[Ewald summation#Particle mesh Ewald (PME) method|particle mesh Ewald]]-based methods.<ref>
Desmond can compute energies and forces<ref>{{cite journal|
{{cite journal
author=Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror, and David E. Shaw|
|doi=10.1109/TSP.2009.2035984
title=Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field|
|bibcode=2010ITSP...58.1122B
url=http://www3.interscience.wiley.com/journal/123314867/abstract?CRETRY=1&SRETRY=0|
|title=Improved Twiddle Access for Fast Fourier Transforms
doi=10.1002/prot.22711|
|journal=IEEE Transactions on Signal Processing
journal=Proteins: Structure, Function, and Bioinformatics|
volume=78|
|volume=58
|issue=3
pmc=2970904|
pages=1950–1958|
|pages=1122–1130
year=2010|
|year=2010
|last1=Bowers
pmid=20408171|
|first1=K.J.
issue=8
|last2=Lippert
}}</ref> for many standard fixed-charged [[Force field (chemistry)|force fields]] used in biomolecular simulations, and is also compatible with polarizable force fields based on the [[Drude model|Drude]] formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (Andersen, [[Nosé-Hoover thermostat|Nosé-Hoover]], and [[Langevin dynamics|Langevin]]) and pressure control ([[Berendsen thermostat|Berendsen]], Martyna-Tobias-Klein, and Langevin). The code also supports methods for restraining atomic positions as well as molecular configurations; allows simulations to be carried out using a variety of periodic cell configurations; and has facilities for accurate checkpointing and restart.
|first2=R.A.
|last3=Dror
|first3=R.O.
|last4=Shaw
|first4=D.E.
|s2cid=17240443
}}</ref><ref>
{{cite journal
|doi=10.1063/1.1839571
|pmid=15740304
|bibcode=2005JChPh.122e4101S
|title=Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
|journal=The Journal of Chemical Physics
|volume=122
|issue=5
|pages=054101
|year=2005
|last1=Shan
|first1=Yibing
|last2=Klepeis
|first2=John L.
|last3=Eastwood
|first3=Michael P.
|last4=Dror
|first4=Ron O.
|last5=Shaw
|first5=David E.
|s2cid=35865319
}}</ref> Constraints can be enforced using the [[M-SHAKE#The M-SHAKE algorithm|M-SHAKE]] algorithm. These methods can be used together with time-scale splitting (RESPA-based) integration schemes.


Desmond can compute energies and forces<ref>
Desmond can also be used to perform absolute and relative free energy calculations. Other simulation techniques (such as [[Parallel tempering|replica exchange]]) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.
{{cite journal
|doi=10.1002/prot.22711
|pmc=2970904
|pmid=20408171
|title=Improved side-chain torsion potentials for the Amber ff99SB protein force field
|journal=Proteins: Structure, Function, and Bioinformatics
|volume=78
|issue=8
|pages=1950–8
|year=2010
|last1=Lindorff-Larsen
|first1=Kresten
|last2=Piana
|first2=Stefano
|last3=Palmo
|first3=Kim
|last4=Maragakis
|first4=Paul
|last5=Klepeis
|first5=John L.
|last6=Dror
|first6=Ron O.
|last7=Shaw
|first7=David E.
}}</ref> for many standard fixed-charged [[Force field (chemistry)|force fields]] used in biomolecular simulations, and is also compatible with polarizable force fields based on the [[Drude model|Drude]] formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control ([[Andersen thermostat]], [[Nosé-Hoover thermostat|Nosé-Hoover]], and [[Langevin dynamics|Langevin]]) and pressure control ([[Berendsen thermostat|Berendsen]], [[Martyna-Tobias-Klein barostat|Martyna-Tobias-Klein]], 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.


Desmond can also be used to perform absolute and relative free energy calculations (e.g., [[free energy perturbation]]). Other simulation methods (such as [[Parallel tempering|replica exchange]]) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.
== Related software tools ==


Desmond is also available in a [[graphics processing unit]] (GPU) accelerated version that is about 60-80 times faster than the [[central processing unit]] (CPU) version.
In addition to the molecular dynamics program, the Desmond software also includes tools for minimization and energy analysis, both of which can be run efficiently in a parallel environment.


==Related software tools==
Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr. Viparr currently supports several versions of the [[CHARMM#CHARMM_force_fields|CHARMM]], [[AMBER#Force_field|Amber]] and [[OPLS]] force fields, as well as a range of different [[water model]]s.


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.
Desmond is integrated with a molecular modeling environment for setting up simulations of biological and chemical systems, and is compatible with [[Visual Molecular Dynamics|VMD]] for trajectory viewing and analysis.


Force fields parameters can be assigned using a template-based parameter assignment tool called [[Viparr]].<ref>{{cite web | url=https://github.com/DEShawResearch/viparr | title=DEShawResearch/Viparr | website=[[GitHub]] }}</ref> It currently supports several versions of the [[CHARMM#CHARMM force fields|CHARMM]], [[AMBER#Force field|Amber]] and [[OPLS]] force fields, and a range of different [[water model]]s.
== See also ==

* [[Molecular dynamics]]
Desmond is integrated with a molecular modeling environment ([[Schrödinger Maestro|Maestro]], developed by [[Schrödinger (company)|Schrödinger, Inc.]]) for setting up simulations of biological and chemical systems, and is compatible with [[Visual Molecular Dynamics]] (VMD) for trajectory viewing and analysis.
* [[List of software for molecular mechanics modeling|Software for molecular mechanics modeling]]

* [[Molecular design software]]
==See also==
* [[Folding@home]]
* [[Comparison of software for molecular mechanics modeling]]
* [[Metadynamics]]


==References==
==References==

{{Reflist}}
{{Reflist}}


== External links ==
==External links==
*[http://deshawresearch.com/resources.html Desmond Website]
*{{Official website|deshawresearch.com}}
*[http://groups.google.com/group/desmond-md-users?lnk=srg&hl=en Desmond Users Group]
*[https://groups.google.com/group/desmond-md-users?lnk=srg&hl=en Desmond Users Group] (deleted)
*[http://www.schrodinger.com/desmond Schrödinger Desmond Product Page]

{{Chemistry software}}


[[Category:Molecular dynamics software]]
[[Category:Molecular dynamics software]]
[[Category:Force fields]]
[[Category:Force fields (chemistry)]]

Latest revision as of 08:45, 21 August 2024

Desmond
Developer(s)D. E. Shaw Research
Operating systemLinux
Platformx86, x86-64, computer clusters
Available inEnglish
TypeComputational chemistry
LicenseProprietary freeware, commercial software
Websitewww.deshawresearch.com/resources_desmond.html, schrodinger.com/desmond

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters.[1][2][3][4] The code uses novel parallel algorithms[5] and numerical methods[6] to achieve high performance on platforms containing multiple processors,[7] but may also be executed on a single computer.

The core and source code are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the Folding@home distributed computing project. Desmond is available as commercial software through Schrödinger, Inc.

Molecular dynamics program

[edit]

Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle mesh Ewald-based methods.[8][9] Constraints can be enforced using the M-SHAKE algorithm. These methods can be used together with time-scale splitting (RESPA-based) integration schemes.

Desmond can compute energies and forces[10] for many standard fixed-charged force fields used in biomolecular simulations, and is also compatible with polarizable force fields based on the Drude formalism. A variety of integrators and support for various ensembles have been implemented in the code, including methods for temperature control (Andersen thermostat, Nosé-Hoover, and Langevin) and pressure control (Berendsen, Martyna-Tobias-Klein, 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.

Desmond can also be used to perform absolute and relative free energy calculations (e.g., free energy perturbation). Other simulation methods (such as replica exchange) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models.

Desmond is also available in a graphics processing unit (GPU) accelerated version that is about 60-80 times faster than the central processing unit (CPU) version.

[edit]

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.

Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr.[11] It currently supports several versions of the CHARMM, Amber and OPLS force fields, and a range of different water models.

Desmond is integrated with a molecular modeling environment (Maestro, developed by Schrödinger, Inc.) for setting up simulations of biological and chemical systems, and is compatible with Visual Molecular Dynamics (VMD) for trajectory viewing and analysis.

See also

[edit]

References

[edit]
  1. ^ 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). "Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters" (PDF). ACM/IEEE SC 2006 Conference (SC'06). p. 43. doi:10.1109/SC.2006.54. ISBN 978-0-7695-2700-0. Archived from the original (PDF) on 2008-08-28. Retrieved 2009-01-16.
  2. ^ Jensen, M. O.; Borhani, D. W.; Lindorff-Larsen, K.; Maragakis, P.; Jogini, V.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. (2010). "Principles of conduction and hydrophobic gating in K+ channels". Proceedings of the National Academy of Sciences. 107 (13): 5833–5838. Bibcode:2010PNAS..107.5833J. doi:10.1073/pnas.0911691107. PMC 2851896. PMID 20231479.
  3. ^ Dror, R. O.; Arlow, D. H.; Borhani, D. W.; Jensen, M. O.; Piana, S.; Shaw, D. E. (2009). "Identification of two distinct inactive conformations of the 2-adrenergic receptor reconciles structural and biochemical observations". Proceedings of the National Academy of Sciences. 106 (12): 4689–4694. Bibcode:2009PNAS..106.4689D. doi:10.1073/pnas.0811065106. PMC 2650503. PMID 19258456.
  4. ^ Shan, Y.; Seeliger, M. A.; Eastwood, M. P.; Frank, F.; Xu, H.; Jensen, M. O.; Dror, R. O.; Kuriyan, J.; Shaw, D. E. (2009). "A conserved protonation-dependent switch controls drug binding in the Abl kinase". Proceedings of the National Academy of Sciences. 106 (1): 139–144. Bibcode:2009PNAS..106..139S. doi:10.1073/pnas.0811223106. PMC 2610013. PMID 19109437.
  5. ^ Bowers, Kevin J.; Dror, Ron O.; Shaw, David E. (2006). "The midpoint method for parallelization of particle simulations". The Journal of Chemical Physics. 124 (18): 184109. Bibcode:2006JChPh.124r4109B. doi:10.1063/1.2191489. PMID 16709099.
  6. ^ Lippert, Ross A.; Bowers, Kevin J.; Dror, Ron O.; Eastwood, Michael P.; Gregersen, Brent A.; Klepeis, John L.; Kolossvary, Istvan; Shaw, David E. (2007). "A common, avoidable source of error in molecular dynamics integrators". The Journal of Chemical Physics. 126 (4): 046101. Bibcode:2007JChPh.126d6101L. doi:10.1063/1.2431176. PMID 17286520. S2CID 38661350.
  7. ^ Edmond Chow; Charles A. Rendleman; Kevin J. Bowers; Ron O. Dror; Douglas H. Hughes; Justin Gullingsrud; Federico D. Sacerdoti; David E. Shaw (July 2008). "Desmond Performance on a Cluster of Multicore Processors". D. E. Shaw Research Technical Report DESRES/TR--2008-01. {{cite journal}}: Cite journal requires |journal= (help)
  8. ^ Bowers, K.J.; Lippert, R.A.; Dror, R.O.; Shaw, D.E. (2010). "Improved Twiddle Access for Fast Fourier Transforms". IEEE Transactions on Signal Processing. 58 (3): 1122–1130. Bibcode:2010ITSP...58.1122B. doi:10.1109/TSP.2009.2035984. S2CID 17240443.
  9. ^ 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". The Journal of Chemical Physics. 122 (5): 054101. Bibcode:2005JChPh.122e4101S. doi:10.1063/1.1839571. PMID 15740304. S2CID 35865319.
  10. ^ Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L.; Dror, Ron O.; Shaw, David E. (2010). "Improved side-chain torsion potentials for the Amber ff99SB protein force field". Proteins: Structure, Function, and Bioinformatics. 78 (8): 1950–8. doi:10.1002/prot.22711. PMC 2970904. PMID 20408171.
  11. ^ "DEShawResearch/Viparr". GitHub.
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