2018
DOI: 10.1038/nmeth.4638
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NAMD goes quantum: an integrative suite for hybrid simulations

Abstract: Applications of hybrid QM/MM methods range from reactions in active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD/VMD with the quantum chemistry packages ORCA, and MOPAC, we provide an integrated, comprehensive, customizable, and easy-to-use suite. Through the QwikMD interface, setup, execution, visualization, and analysis are streamlined for all levels of expertise.

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Cited by 194 publications
(201 citation statements)
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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%
“…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%
“…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%
“…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%