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GROMACS: Fast, flexible, and free

Van Der Spoel, David, Lindahl, Erik, Hess, Berk, Groenhof, Gerrit, Mark, Alan E., Berendsen, Herman J. C.·2005·Journal of Computational Chemistry

DOI 10.1002/jcc.20291

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Abstract

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum‐chemical packages (MOPAC, GAMES‐UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1701–1718, 2005

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Show all 6 references

‘GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers’
Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015) · SoftwareX · doi:10.1016/j.softx.2015.06.001 · Cited by 27,190
Self-citation
Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis
Kagan, V. E., Mao, G., Qu, F., Angeli, J. P. F., Doll, S., Croix, C. S., Dar, H. H., Liu, B., Tyurin, V. A., Ritov, V. B., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2238 · Cited by 3,029
Martini 3: A general purpose force field for coarse-grained molecular dynamics
Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01098-3 · Cited by 1,551
Macromolecular modeling and design in Rosetta: recent methods and frameworks
Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0848-2 · Cited by 888
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Noé, F., Schütte, C., Vanden-Eijnden, E., Reich, L., & Weikl, T. R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905466106 · Cited by 820
Massively parallel de novo protein design for targeted therapeutics
Chevalier, A., Silva, D.-A., Rocklin, G. J., Hicks, D. R., Vergara, R., Murapa, P., Bernard, S. M., Zhang, L., Lam, K.-H., Yao, G., et al. (2017) · Nature · doi:10.1038/nature23912 · Cited by 453
Coarse master equations for peptide folding dynamics
Buchete, N.-V., & Hummer, G. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp0761665 · Cited by 477
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Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications.
Christensen, A. S., Kubař, T., Cui, Q., & Elstner, M. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00584 · Cited by 446
Drug–target affinity prediction using graph neural network and contact maps
Jiang, M., Li, Z., Zhang, S., Wang, S., Wang, X., Yuan, Q., & Wei, Z. (2020) · RSC Advances · doi:10.1039/d0ra02297g · Cited by 372
Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver
Miao, L., Lin, J., Huang, Y., Li, L., Delcassian, D., Ge, Y., Shi, Y., & Anderson, D. G. (2020) · Nature Communications · doi:10.1038/s41467-020-16248-y · Cited by 343
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
Mobley, D. L., Chodera, J. D., & Dill, K. A. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2221683 · Cited by 316
Variational approach to molecular kinetics
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Faelber, K., Posor, Y., Gao, S., Held, M., Roske, Y., Schulze, D., Haucke, V., Noé, F., & Daumke, O. (2011) · Nature · doi:10.1038/nature10369 · Cited by 301
Determination of reaction coordinates via locally scaled diffusion map
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Gault, J., Liko, I., Landreh, M., Shutin, D., Bolla, J. R., Jefferies, D., Agasid, M., Yen, H.-Y., Ladds, M. J. G. W., Lane, D. P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0821-0 · Cited by 171
Terahertz Spectroscopic Analysis of Peptides and Proteins
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Self-citation
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Karatrantos, A., Composto, R. J., Winey, K. I., Kröger, M., & Clarke, N. (2012) · Macromolecules · doi:10.1021/ma3007637 · Cited by 53
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Baiz, C. R., Lin, Y.-S., Peng, C. S., Beauchamp, K. A., Voelz, V. A., Pande, V. S., & Tokmakoff, A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.02.008 · Cited by 51
Direct observation of anisotropic growth of water films on minerals driven by defects and surface tension
Yalcin, S. E., Legg, B. A., Yeşilbaş, M., Malvankar, N. S., & Boily, J.-F. (2020) · Science Advances · doi:10.1126/sciadv.aaz9708 · Cited by 50
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Kagawa, T. F., O'Connell, M. R., Mouat, P., Paoli, M., O'Toole, P. W., & Cooney, J. C. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.12.074 · Cited by 50
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Authors: Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C.
Venue: Journal of Computational Chemistry
Publisher: Wiley
Published: 2005-10-06
Volume: 26
Issue: 16
Pages: 1701-1718
ISSN: 0192-8651 (ISSN-L)
1096-987X
DOI: 10.1002/jcc.20291
OpenAlex: W2171268876
Cited by: 19,182
References: 6
FWCI: 134.72
Type: journal article
Language: en
Open access: closed

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