Interfacing the GROMOS (bio)molecular simulation software to quantum‐chemical program packages

Meier, Katharina; Schmid, Nathan; Gunsteren, Wilfred F. van

doi:10.1002/jcc.23047

Cited by 21 publications

(26 citation statements)

References 48 publications

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“…76 and the similar TIP3P model while Meier et al . 32 report a much longer D–A distance and smaller bond angle a (OH··O). We confirmed that a steepest-descent geometry optimization starting from the geometry reported by Meier et al .…”

Section: Numerical Accuracy and Performancementioning

confidence: 97%

“…30 employed density fitting (also called RI- J approximation) for their BP86/TZVP and BLYP/aug-ccpVQZ calculations which slightly affects energetics and geometries while Meier et al . 32 used a simple steepest descent algorithm with the energy as convergence criterium for their geometry optimizations. The latter can be problematic as can be seen from the purely classical SPC results for which we obtain a binding energy and D–A distance in agreement with Jor-gensen et al .…”

Section: Numerical Accuracy and Performancementioning

confidence: 99%

“…We confirmed that a steepest-descent geometry optimization starting from the geometry reported by Meier et al . 32 remains in the vicinity of the starting point. The values reported by Meier et al .…”

Section: Numerical Accuracy and Performancementioning

confidence: 99%

“…It also immediately benefits the existing user base of the simulation package who can continue to use their software infrastructure such as automated workflow schemes that rely on established input and output syntax. Consequently, several such interfaces have been developed and described in the literature 20–32 . With the exception of PUPIL 33 and the scripting environment ChemShell 34,35 , however, these are mostly limited to support only one specific electronic structure program.…”

Section: Introductionmentioning

confidence: 99%

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An extensible interface for QM/MM molecular dynamics simulations with AMBER

2013

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We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.

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Section: Numerical Accuracy and Performancementioning

confidence: 97%

Section: Numerical Accuracy and Performancementioning

confidence: 99%

Section: Numerical Accuracy and Performancementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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An extensible interface for QM/MM molecular dynamics simulations with AMBER

2013

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“…GROMOS kann an die ausführbaren Dateien der quantenchemischen Programmpakete MNDO [110] und TURBOMOLE [117] gekoppelt werden. [113] Als Startstrukturen wurden die entsprechenden Kristallstrukturen der Dimere EcCM (PDB-Eintrag 1ECM) [96] und PchB (PDB-Eintrag 3HGX) [97] Die Abstandsanalyse zeigt, dass EcCM und PchB beide nicht in der Lage sind, die "nicht-natürlichen" Substrate, Isochorismat für EcCM (obere zwei Zeilen, vierte Spalte) und Chorismat für PchB (untere zwei Zeilen, erste Spalte) in eine Konformation zu überführen, in der die "nichtnatürliche" Reaktion wahrscheinlicher ist.…”

Section: Molekulares Modell Und Berechnungsverfahrenunclassified

Biomolekulare Simulationen mit mehreren Auflösungsniveaus: ein Überblick über methodische Aspekte

Meier¹,

Choutko²,

Dolenc³

et al. 2013

Angewandte Chemie

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Theoretische und computergestützte Modellierungen, die der Erklärung experimenteller Beobachtungen im Hinblick auf ein bestimmtes chemisches Phänomen oder einen bestimmten chemischen Prozess dienen, erfordern eine Reihe von Annahmen. Diese Annahmen betreffen die essentiellen Freiheitsgrade, die Art der Wechselwirkungen und die Erzeugung eines Boltzmann‐Ensembles oder einer Konfigurationstrajektorie. Abhängig von den Freiheitsgraden, die für den interessierenden Prozess unabdingbar sind, wie z. B. elektronische, nukleare oder atomare, molekulare oder supramolekulare, müssen quantenmechanische oder klassisch‐mechanische Bewegungsgleichungen angewendet werden. In Simulationen mit unterschiedlichen Auflösungsniveaus werden verschiedene Ebenen wie elektronische, atomare, supraatomare oder supramolekulare Ebenen in einem einzigen Modell vereint. Dies erlaubt eine Steigerung der Recheneffizienz, wobei eine ausreichende Genauigkeit im Hinblick auf die bestimmten Freiheitsgrade erhalten bleibt. Im Folgenden wird ein Überblick über die grundlegenden Herausforderungen und Annahmen in Bezug auf Modellierungen mit unterschiedlichen Auflösungsniveaus gegeben. Zur Veranschaulichung werden die unterschiedlichen katalytischen Eigenschaften zweier Enzyme, die sich in ihrer Struktur ähneln, jedoch unterschiedliche Substrate binden, im Hinblick auf diese Substrate unter Verwendung von Simulationen mit elektronischen, atomaren und supramolekularen Auflösungsniveaus untersucht.

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Multi‐Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues

Meier¹,

Choutko²,

Dolenc³

et al. 2013

Angew Chem Int Ed

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Theoretical-computational modeling with an eye to explaining experimental observations in regard to a particular chemical phenomenon or process requires choices concerning essential degrees of freedom and types of interactions and the generation of a Boltzmann ensemble or trajectories of configurations. Depending on the degrees of freedom that are essential to the process of interest, for example, electronic or nuclear versus atomic, molecular or supra-molecular, quantum- or classical-mechanical equations of motion are to be used. In multi-resolution simulation, various levels of resolution, for example, electronic, atomic, supra-atomic or supra-molecular, are combined in one model. This allows an enhancement of the computational efficiency, while maintaining sufficient detail with respect to particular degrees of freedom. The basic challenges and choices with respect to multi-resolution modeling are reviewed and as an illustration the differential catalytic properties of two enzymes with similar folds but different substrates with respect to these substrates are explored using multi-resolution simulation at the electronic, atomic and supra-molecular levels of resolution.

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Interfacing the GROMOS (bio)molecular simulation software to quantum‐chemical program packages

Cited by 21 publications

References 48 publications

An extensible interface for QM/MM molecular dynamics simulations with AMBER

An extensible interface for QM/MM molecular dynamics simulations with AMBER

Biomolekulare Simulationen mit mehreren Auflösungsniveaus: ein Überblick über methodische Aspekte

Multi‐Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues

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