ArticleJournal of molecular modeling2018
COBRAMM 2.0 - A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations.
Article in Journal of molecular modeling, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- A QM/MM study on triplet decay of 6-thioguanine and 6-selenoguanine with explicit solvent.Journal of molecular modeling · 2026Article
- A Twist in Electronic Relaxation of Pyrimidine Nucleosides and Nucleotides: Impact of C5 Methylation on Nonadiabatic Transition and Photohydration Damage.Journal of the American Chemical Society · 2026Article
- A fluorescent probe under the microscope showing dual recognition of B-DNA and G-quadruplex DNA.Communications chemistry · 2026Article
- Modern Quantum Chemistry Methodology for PredictingInternational journal of molecular sciences · 2026Review
- Mapping Excited-State Decay Mechanisms in Acetylacetone by Sub-20 fs Time-Resolved Photoelectron Spectroscopy.Journal of the American Chemical Society · 2025Article
- Roadmap for Molecular Benchmarks in Nonadiabatic Dynamics.The journal of physical chemistry. A · 2025Review
- Vibrational Spectroscopy Through Time Averaged Fourier Transform of Autocorrelated Molecular Dynamics Data: Introducing the Free SEMISOFT Web-Platform.Journal of computational chemistry · 2025Article
- Legion: A Platform for Gaussian Wavepacket Nonadiabatic Dynamics.Journal of chemical theory and computation · 2025Article
- Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state.Nature communications · 2024Article
- Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct.Nature communications · 2024Article
- Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size.Journal of chemical theory and computation · 2023Article
- The OpenMolcasJournal of chemical theory and computation · 2023Article
- Double Thionated Pyrimidine Nucleobases: Molecular Tools with Tunable Photoproperties.Journal of the American Chemical Society · 2023Article
- Enhanced Solid-State Fluorescence of Flavin Derivatives by Incorporation in the Metal-Organic Frameworks MIL-53(Al) and MOF-5.Molecules (Basel, Switzerland) · 2023Article
- Modus Operandi of a Pedalo-Type Molecular Switch: Insight from Dynamics and Theoretical Spectroscopy.Molecules (Basel, Switzerland) · 2023Article
- Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles.Journal of chemical theory and computation · 2022Article
- Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM.Journal of computational chemistry · 2022Article
- Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan.Journal of the American Chemical Society · 2022Article
- Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2022Article
- Tracking excited state decay mechanisms of pyrimidine nucleosides in real time.Nature communications · 2021Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results.
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