NAMD goes quantum: an integrative suite for hybrid simulations

Melo, Marcelo C.R.; Bernardi, Rafael C.; Rudack, Till; Scheurer, Maximilian; Riplinger, Christoph; Phillips, J. C.; Maia, Julio D.C.; Rocha, Gerd B.; Ribeiro, João V.; Stone, John E.; Neese, Frank; Schulten, Klaus; Luthey‐Schulten, Zaida

doi:10.1038/nmeth.4638

Cited by 180 publications

(201 citation statements)

References 41 publications

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“…In addition, MD software packages are by now equipped with a plethora of algorithms to access free energy surfaces along simple internal coordinates as well as along collective variables. This information, coupled to the hybrid quantum mechanical/classical MD simulations, allows to study the chemical reactions in complex, anisotropic environments . Under the hypothesis that the chosen collective variable(s) dynamics can be associated with a Markov process, one could set up a Fokker–Planck/Smoluchowski—or the associated Langevin/Brownian—equation to access kinetic information of reactions .…”

Section: Introductionmentioning

confidence: 99%

DiTe2: Calculating the diffusion tensor for flexible molecules

2018

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We report on an extended hydrodynamic modeling of the friction tensorial properties of flexible molecules including all types of natural, Z‐Matrix like, internal coordinates. We implement the new methodology by extending and updating the software DiTe [Barone et al. J. Comput. Chem. 30, 2 (2009)]. DiTe (DIffusion TEnsor) implements a hydrodynamic modeling of the generalized translational, rotational, and configurational friction and diffusion tensors of flexible molecules in which flexibility is described in terms of dihedral angles. The new tool, DiTe2, has been renewed to include also stretching and bending types of internal mobility. Furthermore, DiTe2 is able to calculate the friction and diffusion tensors along collective (or reaction) coordinates defined as linear combinations of the internal natural ones. A number of tests are reported to show the new features of DiTe2. As leitmotiv for the tests, the calmodulin protein is taken into consideration, described both at all‐atom and coarse‐grained levels. © 2018 Wiley Periodicals, Inc.

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Section: Introductionmentioning

confidence: 99%

DiTe2: Calculating the diffusion tensor for flexible molecules

2018

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“…Through the continuous raise of computer power, larger molecular systems become available to be studied by molecular simulations . The associated progress in hybrid method development combining QM with MM simulation allows studying active sites in small enzymes and large macromolecular complexes . Thus, LMA is well suited as an IR spectroscopy tool applicable for almost all kinds of molecular systems.…”

Section: Resultsmentioning

confidence: 99%

“…42 The associated progress in hybrid method development combining QM with MM simulation allows studying active sites in small enzymes and large macromolecular complexes. 43 Thus, LMA is well suited as an IR spectroscopy tool applicable for almost all kinds of molecular systems. We anticipate LMA to be beneficial to evaluate spectra and to initiate further experiments to test hypotheses about underlying protein function.…”

Section: Resultsmentioning

confidence: 99%

Monitoring transient events in infrared spectra using local mode analysis

et al. 2018

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Time-resolved Fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with infrared (IR) spectral features and vice versa. Here, we present the python-based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA). Deuterated MA exists in two almost equally populated tautomeric states separated by a low barrier for proton transfer so IR spectra represent a mixture of both states. By state-dependent LMA, we obtain pure spectra for each tautomeric state occurring within the quantum mechanics trajectory. By time-resolved LMA, we obtain a clear view of the transition between states in the spectrum. Through local mode decomposition and the band-pass filter, marker bands for each state are identified. Thus, LMA is beneficial to analyze the experimental spectra based on a mixture of states by determining the individual contributions to the spectrum and motion of each state.

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“…The method used here of electrostatic embedding, that is, electrostatic interactions between QM and MM atoms, was described in detail in the literature [ 29 ] and online documents. [ 30 ] In short, the partial charges of MM atoms surrounding all QM atoms are used to approximate the electrostatic environment where QM atoms are found.…”

Section: Methodsmentioning

confidence: 99%

“…With each subunit, QM‐MM simulations were carried out with NAMD QM‐MM software, [ 29 ] based on NAMD software [ 31 ] and linked to ORCA software, [ 32 ] version 4.1.1. Conditions were temp 300 K and pressure 1.01325 bar, with the following flags: ts = 0.5 fs, cutoff = 12.0 Å, pairlistdist = 14.0 Å, switchdist = 10.0 Å. BS simulations were carried out with ORCA software standalone [ 32 ] by using the flip spin method, flipping, in turn, either Fe77 or Fe78.…”

Section: Methodsmentioning

confidence: 99%

A New Route for Dioxygen Activation Uncovered from Quantum Mechanics Investigations of X‐Ray‐Diffraction‐Captured Intermediates of the Ferroxidase Reaction of Ferritins from Gram‐Negative Bacteria

Pietra¹

2020

Advcd Theory and Sims

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Following the recent reassessment from X‐ray‐diffraction‐caught short‐path uptake to wide permeation of the S20A mutant Escherichia coli ferritin by ferrous ions, what happens when dioxygen gets to the diiron system is investigated. It is shown that the previously X‐ray‐caught situation of an unbound‐dioxygen diferrous state actually is an ephemeral state that changes into a P‐type peroxodiferric state, while a water molecule moves to bridge the two ferric ions, in what appears to be a remarkable redox process. All this stems from density functional theory (DFT)‐based quantum mechanics‐molecular mechanics and broken symmetry (BS) calculations that are extended to X‐ray‐diffraction‐caught oxodiferric and I‐type peroxodiferric systems from other subunits of the same crystal structure, validating them while determining antiferromagnetic coupling with all such diiron systems except the oxodiferric one. The latter converged, on BS, to ferromagnetic coupling under a wide variety of hybrid DFT functionals and basis sets. The trend of the Heisenberg J coupling reflects and substantiates the structures of the diiron core.

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NAMD goes quantum: an integrative suite for hybrid simulations

Cited by 180 publications

References 41 publications

DiTe2: Calculating the diffusion tensor for flexible molecules

DiTe2: Calculating the diffusion tensor for flexible molecules

Monitoring transient events in infrared spectra using local mode analysis

A New Route for Dioxygen Activation Uncovered from Quantum Mechanics Investigations of X‐Ray‐Diffraction‐Captured Intermediates of the Ferroxidase Reaction of Ferritins from Gram‐Negative Bacteria

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