NAMD goes quantum: an integrative suite for hybrid simulations
MARCELO R. S. MELO
1, 2
,
Rafael C Bernardi
1
,
Till Rudack
1, 3
,
Maximilian Scheurer
4, 5
,
Christoph Riplinger
6
,
James C. Phillips
1
,
Julio D C Maia
7
,
Gerd B. Rocha
8
,
João V Ribeiro
1
,
John E. Stone
1
,
Frank Neese
9
,
Klaus Schulten
1, 10
,
Zaida Luthey‐Schulten
1, 2, 10, 11
5
Interdisciplinary Center for Scientific Computing, Heidelberg, Germany
|
6
FAccTs GmbH, Köln, Germany
|
Publication type: Journal Article
Publication date: 2018-03-26
scimago Q1
wos Q1
SJR: 17.251
CiteScore: 49.0
Impact factor: 32.1
ISSN: 15487091, 15487105
PubMed ID:
29578535
Biochemistry
Molecular Biology
Cell Biology
Biotechnology
Abstract
The integration of quantum chemistry and molecular dynamics programs coupled with a graphical user interface provides a streamlined tool for powerful simulations of biomolecular reaction mechanisms. Hybrid methods that combine quantum mechanics (QM) and molecular mechanics (MM) can be applied to studies of reaction mechanisms in locations ranging from active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD and VMD with the quantum chemistry packages ORCA and MOPAC, we created an integrated, comprehensive, customizable, and easy-to-use suite ( http://www.ks.uiuc.edu/Research/qmmm ). Through the QwikMD interface, setup, execution, visualization, and analysis are streamlined for all levels of expertise.
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Citations from 2025:
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MELO M. R. S. et al. NAMD goes quantum: an integrative suite for hybrid simulations // Nature Methods. 2018. Vol. 15. No. 5. pp. 351-354.
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MELO M. R. S., Bernardi R. C., Rudack T., Scheurer M., Riplinger C., Phillips J. C., Maia J. D. C., Rocha G. B., Ribeiro J. V., Stone J. E., Neese F., Schulten K., Luthey‐Schulten Z. NAMD goes quantum: an integrative suite for hybrid simulations // Nature Methods. 2018. Vol. 15. No. 5. pp. 351-354.
Cite this
RIS
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TY - JOUR
DO - 10.1038/nmeth.4638
UR - https://doi.org/10.1038/nmeth.4638
TI - NAMD goes quantum: an integrative suite for hybrid simulations
T2 - Nature Methods
AU - MELO, MARCELO R. S.
AU - Bernardi, Rafael C
AU - Rudack, Till
AU - Scheurer, Maximilian
AU - Riplinger, Christoph
AU - Phillips, James C.
AU - Maia, Julio D C
AU - Rocha, Gerd B.
AU - Ribeiro, João V
AU - Stone, John E.
AU - Neese, Frank
AU - Schulten, Klaus
AU - Luthey‐Schulten, Zaida
PY - 2018
DA - 2018/03/26
PB - Springer Nature
SP - 351-354
IS - 5
VL - 15
PMID - 29578535
SN - 1548-7091
SN - 1548-7105
ER -
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@article{2018_MELO,
author = {MARCELO R. S. MELO and Rafael C Bernardi and Till Rudack and Maximilian Scheurer and Christoph Riplinger and James C. Phillips and Julio D C Maia and Gerd B. Rocha and João V Ribeiro and John E. Stone and Frank Neese and Klaus Schulten and Zaida Luthey‐Schulten},
title = {NAMD goes quantum: an integrative suite for hybrid simulations},
journal = {Nature Methods},
year = {2018},
volume = {15},
publisher = {Springer Nature},
month = {mar},
url = {https://doi.org/10.1038/nmeth.4638},
number = {5},
pages = {351--354},
doi = {10.1038/nmeth.4638}
}
Cite this
MLA
Copy
MELO, MARCELO R. S., et al. “NAMD goes quantum: an integrative suite for hybrid simulations.” Nature Methods, vol. 15, no. 5, Mar. 2018, pp. 351-354. https://doi.org/10.1038/nmeth.4638.