Desmond (software)

Desmond (software)

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. 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 Schrodinger.

Contents

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. 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.

Related software tools

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 for setting up simulations of biological and chemical systems, and is 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". Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006. (ACM). ISBN 0-7695-2700-0. http://sc06.supercomputing.org/schedule/pdf/pap259.pdf. 
  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 (PNAS) 107 (13): 5833–5838. doi:10.1073/pnas.0911691107. PMC 2851896. PMID 20231479. http://www.pnas.org/content/107/13/5833.full. 
  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 (PNAS) 106 (12): 4689–4694. doi:10.1073/pnas.0811065106. PMC 2650503. PMID 19258456. http://www.pnas.org/content/106/12/4689.full. 
  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 (PNAS) 106 (1): 139–144. doi:10.1073/pnas.0811223106. PMC 2610013. PMID 19109437. http://www.pnas.org/content/106/1/139.full. 
  5. ^ Kevin J. Bowers, Ron O. Dror, and David E. Shaw (2006). "The Midpoint Method for Parallelization of Particle Simulations". Journal of Chemical Physics (J. Chem. Phys.) 124 (18): 184109:1–11. doi:10.1063/1.2191489. PMID 16709099. http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000124000018184109000001&idtype=cvips&gifs=yes. 
  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 (J. Chem. Phys.) 126 (4): 046101:1–2. doi:10.1063/1.2431176. PMID 17286520. http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000126000004046101000001&idtype=cvips&gifs=yes. 
  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. http://deshawresearch.com/publications.html. 
  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 (IEEE) 58 (3): 1122–1130. doi:10.1109/TSP.2009.2035984. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5313934&tag=1. 
  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 (J. Chem. Phys.) 122 (5): 054101:1–13. doi:10.1063/1.1839571. PMID 15740304. http://jcp.aip.org/jcpsa6/v122/i5/p054101_s1. 
  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. http://www3.interscience.wiley.com/journal/123314867/abstract?CRETRY=1&SRETRY=0. 

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