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A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics

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Center for Structural Biology, Department of Chemistry, Vanderbilt University, 5140 Medical Research Building III, 465 21st Avenue South, Nashville, Tennessee 37232-8725, Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, North Carolina 27599-0001, Laboratory of Structural Biology, National Institute of Environmental Health Science, Research Triangle Park, 12 Davis Drive, Chapel Hill, North Carolina 27709-5900, Center for Biophysics and Computational Biology, University of Illinois, 156 Davenport Hall, 607 South Mathews Avenue, Urbana, Illinois 61801-3635, and Department of Biopharmaceutical Sciences, University of California, Byers Hall, 1700 Fourth Street, Suite 501, San Francisco, California 94158-2330
* To whom correspondence should be addressed. Phone: (615) 936-3569. Fax: (615) 936-2211. E-mail: [email protected]
†Vanderbilt University.
‡University of North Carolina.
§National Institute of Environmental Health Science.
∥University of Illinois at Urbana-Champaign.
⊥University of California, San Francisco.
Cite this: J. Chem. Theory Comput. 2008, 4, 10, 1669–1680
Publication Date (Web):September 10, 2008
https://doi.org/10.1021/ct8002173
Copyright © 2008 American Chemical Society
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Abstract

We report a serious problem associated with a number of current implementations of Andersen and Langevin dynamics algorithms. When long simulations are run in many segments, it is sometimes possible to have a repeating sequence of pseudorandom numbers enter the calcuation. We show that, if the sequence repeats rapidly, the resulting artifacts can quickly denature biomolecules and are then easily detectable. However, if the sequence repeats less frequently, the artifacts become subtle and easily overlooked. We derive a formula for the underlying cause of artifacts in the case of the Langevin thermostat, and find it vanishes slowly as the inverse square root of the number of time steps per simulation segment. Numerous examples of simulation artifacts are presented, including dissociation of a tetrameric protein after 110 ns of dynamics, reductions in atomic fluctuations for a small protein in implicit solvent, altered thermodynamic properties of a box of water molecules, and changes in the transition free energies between dihedral angle conformations. Finally, in the case of strong thermocoupling, we link the observed artifacts to previous work in nonlinear dynamics and show that it is possible to drive a 20-residue, implicitly solvated protein into periodic trajectories if the thermostat is not used properly. Our findings should help other investigators re-evaluate simulations that may have been corrupted and obtain more accurate results.

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Illustration of residual Langevin forces, illustration of the dissociation of the apostreptavidin tetramer, demonstration that rapidly restarting simulations with a changing pseudorandom number generator (PRNG) seed permits stable dynamics, clarification of the fact that Langevin artifacts tend to lead to higher protein backbone rmsd relative to the native state but lower atomic fluctuations thereafter, further demonstration of periodic trajectories obtained with PRNG artifacts and strong thermocoupling, and illustrations of Langevin dynamics artifacts in simulations performed with the GROMACS and NAMD codes. This material is available free of charge via the Internet at http://pubs.acs.org.

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  58. A. M. Naserian-Nik, M. Tahani, M. Karttunen. Pulling of double-stranded DNA by atomic force microscopy: a simulation in atomistic details. RSC Advances 2013, 3 (26) , 10516. https://doi.org/10.1039/c3ra23213a
  59. Daniel P. Oehme, Robert T. C. Brownlee, David J. D. Wilson. Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease. Journal of Computational Chemistry 2012, 33 (32) , 2566-2580. https://doi.org/10.1002/jcc.23095
  60. M. L. Dodson, Ross C. Walker, R. Stephen Lloyd, . Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site. PLoS ONE 2012, 7 (2) , e31377. https://doi.org/10.1371/journal.pone.0031377
  61. Richard T. Bradshaw, Pietro G. A. Aronica, Edward W. Tate, Robin J. Leatherbarrow, Ian R. Gould. Mutational Locally Enhanced Sampling (MULES) for quantitative prediction of the effects of mutations at protein–protein interfaces. Chemical Science 2012, 3 (5) , 1503. https://doi.org/10.1039/c2sc00895e
  62. Thomas Caulfield, José L. Medina-Franco. Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A. Journal of Structural Biology 2011, 176 (2) , 185-191. https://doi.org/10.1016/j.jsb.2011.07.015
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  66. Linda Viererblová, Jiří Kolafa, Stanislav Labík, Anatol Malijevský. Virial coefficients and equation of state of the penetrable sphere model. Phys. Chem. Chem. Phys. 2010, 12 (1) , 254-262. https://doi.org/10.1039/B917204A
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