Now showing items 1-8 of 8

    • Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties 

      Beerepoot, Maarten; Steindal, Arnfinn Hykkerud; List, Nanna Holmgaard; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel, 2016-03-03)
      We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specific atom-centered partial charges and isotropic polarizabilities averaged over a large number of geometries of solvent molecules. The use ...
    • A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein 

      Steindal, Arnfinn Hykkerud; Olsen, Jógvan Magnus Haugaard; Ruud, Kenneth; Frediani, Luca; Kongsted, Jacob (Journal article; Tidsskriftartikkel; Peer reviewed, 2012-02-01)
      We present for the first time a QM/MM study of the one- and two-photon absorption spectra of the GFP chromophore embedded in the full protein environment described by an advanced quantum mechanically derived polarizable force field. The calculations are performed on a crystal structure of the green fluorescent protein (GFP) using the polarizable embedding density functional theory (PE-DFT) scheme. ...
    • CPPE: An Open-Source C++ and Python Library for Polarizable Embedding 

      Scheurer, Maximilian; Reinholdt, Peter; Kjellgren, Erik Rosendahl; Olsen, Jógvan Magnus Haugaard; Dreuw, Andreas; Kongsted, Jacob (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-10-03)
      We present a modular open-source library for polarizable embedding (PE) named CPPE. The library is implemented in C++, and it additionally provides a Python interface for rapid prototyping and experimentation in a high-level scripting language. Our library integrates seamlessly with existing quantum chemical program packages through an intuitive and minimal interface. Until now, CPPE has been ...
    • Extreme Scalability of DFT-based QM/MM MD Simulations Using MiMiC 

      Bolnykh, Viacheslav; Olsen, Jógvan Magnus Haugaard; Meloni, Simone; Bircher, Martin Peter; Ippoliti, Emiliano; Carloni, Paolo; Rothlisberger, Ursula (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-09-09)
      We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD ...
    • MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry 

      Olsen, Jógvan Magnus Haugaard; Bolnykh, Viacheslav; Meloni, Simone; Ippoliti, Emiliano; Bircher, Martin Peter; Carloni, Paolo; Rothlisberger, Ursula (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-04-18)
      We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. This allows exploiting the existing parallelization strategies used by the coupled programs while maintaining a ...
    • Molecular quantum mechanical gradients within the polarizable embedding approach-Application to the internal vibrational Stark shift of acetophenone 

      List, Nanna Holmgaard; Beerepoot, Maarten T. P.; Olsen, Jógvan Magnus Haugaard; Gao, Bin; Ruud, Kenneth; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob (Journal article; Tidsskriftartikkel; Peer reviewed, 2015-01-21)
      We present an implementation of analytical quantum mechanical molecular gradients within the polarizable embedding (PE) model to allow for efficient geometry optimizations and vibrational analysis of molecules embedded in large, geometrically frozen environments. We consider a variational ansatz for the quantum region, covering (multiconfigurational) self-consistent-field and Kohn–Sham density ...
    • Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems 

      Steindal, Arnfinn Hykkerud; Beerepoot, Maarten; Ringholm, Magnus; List, Nanna Holmgaard; Ruud, Kenneth; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel; Peer reviewed, 2016-09-19)
      We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree–Fock and Kohn–Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules ...
    • Response properties of embedded molecules through the polarizable embedding model 

      Steinmann, Casper; Reinholdt, Peter; Nørby, Morten Steen; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard (Journal article; Tidsskriftartikkel; Peer reviewed, 2018-09-04)
      The polarizable embedding (PE) model is a fragment‐based quantum‐classical approach aimed at accurate inclusion of environment effects in quantum‐mechanical response property calculations. The aim of this tutorial review is to give insight into the practical use of the PE model. Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to ...