NAMD: Difference between revisions
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It was introduced in 1995 by Nelson ''et al.'' as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores.<ref>{{cite web |title=NAMD: Scalable Molecular Dynamics |url=http://www.ks.uiuc.edu/Research/namd/ |access-date=1 August 2016 |website=Theoretical and Computational Biophysics Group (TCB) |publisher=University of Illinois Urbana-Champaign}}</ref> | It was introduced in 1995 by Nelson ''et al.'' as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores.<ref>{{cite web |title=NAMD: Scalable Molecular Dynamics |url=http://www.ks.uiuc.edu/Research/namd/ |access-date=1 August 2016 |website=Theoretical and Computational Biophysics Group (TCB) |publisher=University of Illinois Urbana-Champaign}}</ref> | ||
NAMD has an interface to [[quantum chemistry]] packages [[ORCA (quantum chemistry program)|ORCA]] and [[MOPAC]], as well as a scripted interface to many other quantum packages.<ref>{{cite web |title=Hybrid QM/MM NAMD |url= | NAMD has an interface to [[quantum chemistry]] packages [[ORCA (quantum chemistry program)|ORCA]] and [[MOPAC]], as well as a scripted interface to many other quantum packages.<ref>{{cite web |title=Hybrid QM/MM NAMD |url=https://www.ks.uiuc.edu/Research/qmmm/ |access-date=26 March 2018 |website=Theoretical and Computational Biophysics Group (TCB) |publisher=University of Illinois Urbana-Champaign}}</ref> Together with [[Visual Molecular Dynamics]] (VMD) and QwikMD,<ref>{{cite journal|title=QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts | ||
|year=2016 |journal=Scientific Reports|doi=10.1038/srep26536 |last1=Ribeiro |first1=João V. |last2=Bernardi |first2=Rafael C. |last3=Rudack |first3=Till |last4=Stone |first4=John E. |last5=Phillips |first5=James C. |last6=Freddolino |first6=Peter L. |last7=Schulten |first7=Klaus |volume=6 | | |year=2016 |journal=Scientific Reports|doi=10.1038/srep26536 |last1=Ribeiro |first1=João V. |last2=Bernardi |first2=Rafael C. |last3=Rudack |first3=Till |last4=Stone |first4=John E. |last5=Phillips |first5=James C. |last6=Freddolino |first6=Peter L. |last7=Schulten |first7=Klaus |volume=6 |article-number=26536 |pmid=27216779 |pmc=4877583 |bibcode=2016NatSR...626536R }}</ref> NAMD's interface provides access to hybrid [[QM/MM]] simulations in an integrated, comprehensive, customizable, and easy-to-use suite.<ref>{{cite journal|title=NAMD goes quantum: an integrative suite for hybrid simulations |year=2018 |journal=Nature Methods|doi=10.1038/nmeth.4638 |last1=Melo |first1=Marcelo C R. |last2=Bernardi |first2=Rafael C. |last3=Rudack |first3=Till |last4=Scheurer |first4=Maximilian |last5=Riplinger |first5=Christoph |last6=Phillips |first6=James C. |last7=Maia |first7=Julio D C. |last8=Rocha |first8=Gerd B. |last9=Ribeiro |first9=João V. |last10=Stone |first10=John E. |last11=Neese |first11=Frank |last12=Schulten |first12=Klaus |last13=Luthey-Schulten |first13=Zaida |volume=15 |issue=5 |pages=351–354 |pmid=29578535 |pmc=6095686 }}</ref> | ||
NAMD is available as [[freeware]] for non-commercial use by individuals, academic institutions, and corporations for in-house business uses. | NAMD is available as [[freeware]] for non-commercial use by individuals, academic institutions, and corporations for in-house business uses. | ||
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* {{Official website|www.ks.uiuc.edu/Research/namd}}, at TCB website | * {{Official website|www.ks.uiuc.edu/Research/namd}}, at TCB website | ||
* [http://charm.cs.uiuc.edu/research/moldyn/ NAMD page at the PPL website] | * [http://charm.cs.uiuc.edu/research/moldyn/ NAMD page at the PPL website] | ||
* [ | * [https://www.nvidia.com/object/namd_on_tesla.html NAMD on GPUs] | ||
{{Chemistry software}} | {{Chemistry software}} | ||
Latest revision as of 17:07, 30 September 2025
Script error: No such module "Infobox".Template:Template other Script error: No such module "Check for unknown parameters".Script error: No such module "Check for conflicting parameters". Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program)[1] is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model (not to be confused with CHARMM). It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms).[2] It has been developed by the collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois Urbana–Champaign.
It was introduced in 1995 by Nelson et al. as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores.[3]
NAMD has an interface to quantum chemistry packages ORCA and MOPAC, as well as a scripted interface to many other quantum packages.[4] Together with Visual Molecular Dynamics (VMD) and QwikMD,[5] NAMD's interface provides access to hybrid QM/MM simulations in an integrated, comprehensive, customizable, and easy-to-use suite.[6]
NAMD is available as freeware for non-commercial use by individuals, academic institutions, and corporations for in-house business uses.
See also
References
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External links
- Script error: No such module "Official website".Script error: No such module "Check for unknown parameters"., at TCB website
- NAMD page at the PPL website
- NAMD on GPUs
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