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== Desmond molecular dynamics program ==
== Desmond 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|
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]]|
|publisher=[[IEEE]]
author=Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, and David E. Shaw|
|author=Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, and David E. Shaw
title=Improved Twiddle Access for Fast Fourier Transforms|
|title=Improved Twiddle Access for Fast Fourier Transforms
url=http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5313934&tag=1|
|url=http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5313934&tag=1
doi=10.1109/TSP.2009.2035984 |
|doi=10.1109/TSP.2009.2035984
journal=IEEE Transactions on Signal Processing|
|journal=IEEE Transactions on Signal Processing
volume=58|
|volume=58
issue=3|
|issue=3
pages=1122–1130|
|pages=1122–1130
year=2010
|year=2010
}}</ref><ref>{{cite journal|
}}</ref><ref>{{cite journal
publisher=[[J. Chem. Phys.]]|
|publisher=[[J. Chem. Phys.]]
author=Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror and David E. Shaw|
|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|
|title=Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation
url=http://jcp.aip.org/jcpsa6/v122/i5/p054101_s1|
|url=http://jcp.aip.org/jcpsa6/v122/i5/p054101_s1
doi=10.1063/1.1839571|
|doi=10.1063/1.1839571
journal=Journal of Chemical Physics|
|journal=Journal of Chemical Physics
volume=122|
|volume=122
pages=054101:1–13|
|pages=054101:1–13
year=2005|
|year=2005
pmid=15740304|
|pmid=15740304
issue=5
|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.
}}</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 can compute energies and forces<ref>{{cite journal|
Desmond can compute energies and forces<ref>{{cite journal
author=Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror, and David E. Shaw|
|author=Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror, and David E. Shaw
title=Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field|
|title=Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field
url=http://www3.interscience.wiley.com/journal/123314867/abstract?CRETRY=1&SRETRY=0|
|url=http://www3.interscience.wiley.com/journal/123314867/abstract?CRETRY=1&SRETRY=0
doi=10.1002/prot.22711|
|doi=10.1002/prot.22711
journal=Proteins: Structure, Function, and Bioinformatics|
|journal=Proteins: Structure, Function, and Bioinformatics
volume=78|
|volume=78
pmc=2970904|
|pmc=2970904
pages=1950–1958|
|pages=1950–1958
year=2010|
|year=2010
pmid=20408171|
|pmid=20408171
issue=8
|issue=8
}}</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.
}}</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.


Desmond can also be used to perform absolute and relative free energy calculations (e.g.,. f[[Free energy perturbation|ree energy perturbation]]). 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.
Desmond can also be used to perform absolute and relative free energy calculations (e.g.,. [[free energy perturbation]]). 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.


There is also a GPU-accelerated version of Desmond available that is approximately 60-80 times faster than the CPU version.
There is also a GPU-accelerated version of Desmond available that is approximately 60-80 times faster than the CPU version.

Revision as of 01:39, 28 October 2015

Desmond
Developer(s)D. E. Shaw Research
Operating systemLinux
TypeComputational Chemistry
LicenseAcademic, Commercial
Websitehttp://www.deshawresearch.com/resources_desmond.html, http://www.schrodinger.com/products/14/3/

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 techniques[6] to achieve high performance on platforms containing a large number of processors,[7] but may also be executed on a single computer.

The core and source code are available without 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 for commercial use through Schrödinger, Inc.

Desmond 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 particle-mesh-based Ewald techniques.[8][9] Constraints can be enforced using the M-SHAKE algorithm. These approaches can be used in combination 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, Nosé-Hoover, and Langevin) and pressure control (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.

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

There is also a GPU-accelerated version of Desmond available that is approximately 60-80 times faster than the 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.

Force fields parameters can be assigned using a template-based parameter assignment tool called Viparr. Viparr currently supports several versions of the CHARMM, Amber and OPLS force fields, as well as 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 also compatible with VMD for trajectory viewing and analysis.

See also

References

  1. ^ 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 (2006). "Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters" (PDF). Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006. ACM. ISBN 0-7695-2700-0.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Morten Ø. Jensen, David W. Borhani, Kresten Lindorff-Larsen, Paul Maragakis, Vishwanath Jogini, Michael P. Eastwood, Ron O. Dror, and David E. Shaw (2010). "Principles of Conduction and Hydrophobic Gating in K+ Channels". Proceedings of the National Academy of Sciences of the United States of America. 107 (13). PNAS: 5833–5838. doi:10.1073/pnas.0911691107. PMC 2851896. PMID 20231479.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, and David E. Shaw (2009). "Identification of Two Distinct Inactive Conformations of the ß2-Adrenergic Receptor Reconciles Structural and Biochemical Observations". Proceedings of the National Academy of Sciences of the United States of America. 106 (12). PNAS: 4689–4694. doi:10.1073/pnas.0811065106. PMC 2650503. PMID 19258456.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, Filipp Frank, Huafeng Xu, Morten Ø. Jensen, Ron O. Dror, John Kuriyan, and David E. Shaw (2009). "A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase". Proceedings of the National Academy of Sciences of the United States of America. 106 (1). PNAS: 139–144. doi:10.1073/pnas.0811223106. PMC 2610013. PMID 19109437.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Kevin J. Bowers, Ron O. Dror, and David E. Shaw (2006). "The Midpoint Method for Parallelization of Particle Simulations". Journal of Chemical Physics. 124 (18). J. Chem. Phys.: 184109:1–11. doi:10.1063/1.2191489. PMID 16709099.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ Ross A. Lippert, Kevin J. Bowers, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, and David E. Shaw (2007). "A Common, Avoidable Source of Error in Molecular Dynamics Integrators". Journal of Chemical Physics. 126 (4). J. Chem. Phys.: 046101:1–2. doi:10.1063/1.2431176. PMID 17286520.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ Edmond Chow, Charles A. Rendleman, Kevin J. Bowers, Ron O. Dror, Douglas H. Hughes, Justin Gullingsrud, Federico D. Sacerdoti, and David E. Shaw (2008). "Desmond Performance on a Cluster of Multicore Processors". D. E. Shaw Research Technical Report DESRES/TR--2008-01, July 2008. {{cite journal}}: Cite journal requires |journal= (help)CS1 maint: multiple names: authors list (link)
  8. ^ Kevin J. Bowers, Ross A. Lippert, Ron O. Dror, and David E. Shaw (2010). "Improved Twiddle Access for Fast Fourier Transforms". IEEE Transactions on Signal Processing. 58 (3). IEEE: 1122–1130. doi:10.1109/TSP.2009.2035984.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror and David E. Shaw (2005). "Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation". Journal of Chemical Physics. 122 (5). J. Chem. Phys.: 054101:1–13. doi:10.1063/1.1839571. PMID 15740304.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ^ Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L. Klepeis, Ron O. Dror, and David E. Shaw (2010). "Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field". Proteins: Structure, Function, and Bioinformatics. 78 (8): 1950–1958. doi:10.1002/prot.22711. PMC 2970904. PMID 20408171.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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