Jógvan Magnus Haugaard Olsen

Technical University of Denmark

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Papers

Citation

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i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Jacob Kongsted

University of Southern Denmark

Peter Reinholdt

University of Southern Denmark

Ursula Röthlisberger

École Polytechnique Fédérale de Lausanne

Casper Steinmann

Aalborg University

Emiliano Ippoliti

Forschungszentrum Jülich

Nanna Holmgaard List

KTH Royal Institute of Technology

David Carrasco‐Busturia

Technical University of Denmark

Kenneth Ruud

UiT The Arctic University of Norway

Simone Meloni

University of Ferrara

Paolo Carloni

Forschungszentrum Jülich

Cooperative Institutions

Aarhus University

Technical University of Denmark

University of Oslo

University of Southern Denmark

University of Copenhagen

Centre National de la Recherche Scientifique

KTH Royal Institute of Technology

UiT The Arctic University of Norway

Linköping University

École Polytechnique Fédérale de Lausanne

Author Statistics

Papers

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PERI–CC2: A Polarizable Embedded RI-CC2 Method

Journal of Chemical Theory and Computation (2012)

Tobias Schwabe Kristian Sneskov Jógvan Magnus Haugaard Olsen Jacob Kongsted Ove Christiansen

We present a combination of the polarizable embedding (PE) method with the resolution-of-the-identity implementation of the approximate coupled-cluster singles and doubles method CC2. The new approach, termed PERI-CC2, allows one to study excited state phenomena of large solvated molecular systems with an accurate correlated wave function method. Central to the PE approach is the advanced description of the environmental electrostatic potential and inclusion of polarization, and the quintessence of RI-CC2 is efficient access to excited state properties while retaining the accuracy associated with CC theory. To maintain efficiency, an approximate truncated CC2 density is introduced to calculate the PE contributions. Explicitly, we derive the central equations and outline an implementation of polarizable embedding for the RI-CC2 approach. The new method is tested against previous PE-CC2 and PE-CCSD results for solvatochromic shifts, demonstrating how the important effects of polarization are incorporated well with PERI-CC2 but with a dramatically reduced overall computational cost. A follow-up investigation of the solvatochromic shift of uracil in aqueous solution further illustrates the potential of PERI-CC2. We discuss the need to explicitly incorporate several water molecules into the region treated by quantum mechanics in order to obtain a reliable and accurate description of the physical effects when specific solute/solvent interactions as, e.g., hydrogen-bonds are involved.

Coupled cluster

Solvatochromism

10.1021/ct3003749

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Citations (74)

Dataset for the article "Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems"

Zenodo (CERN European Organization for Nuclear Research) (2020)

Jógvan Magnus Haugaard Olsen Simen Reine Olav Vahtras Erik Rosendahl Kjellgren Peter Reinholdt

This dataset contains additional material related to the article "Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems". The article is available at https://doi.org/10.1063/1.5144298 (open access).

Note that the current version of the dataset is not complete. The complete dataset will be uploaded as soon as possible.

Python

10.5281/zenodo.3710461

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Dataset for the article "Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments"

Zenodo (CERN European Organization for Nuclear Research) (2019)

Peter Reinholdt Erik Rosendahl Kjellgren Casper Steinmann Jógvan Magnus Haugaard Olsen

This dataset contains additional material related to the article: "Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments". The preprint is available at https://doi.org/10.26434/chemrxiv.8126912. See readme.txt for further description.

10.5281/zenodo.3250839

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MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Jógvan Magnus Haugaard Olsen Viacheslav Bolnykh Simone Meloni Emiliano Ippoliti Martin P. Bircher

<div>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 high degree of flexibility. MiMiC has been used in a new electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) implementation coupling the highly efficient CPMD and GROMACS programs but it can also be extended to use other programs. The framework can also be utilized to extend the partitioning of the system into several domains that can be treated using different models, such as models based on wavefunction or density functional theory as well as coarse-graining and continuum models. The new QM/MM implementation treats long-range electrostatic QM-MM interactions through the multipoles of the QM subsystem which substantially reduces the computational cost without loss of accuracy compared to an exact treatment. This enables QM/MM molecular dynamics (MD) simulations of very large systems.</div>

Granularity

Multiscale Modeling

Electrostatics

10.26434/chemrxiv.7635986

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OpenMM-MiMiC Interface for Efficient and Flexible Multiscale Simulations

arXiv (Cornell University) (2025)

Andrea Levy Andrej Antalík Jógvan Magnus Haugaard Olsen Ursula Röthlisberger

MiMiC is a flexible and efficient framework for multiscale simulations in which different subsystems are treated by individual client programs. In this work, we present a new interface with OpenMM to be used as an MM client program and we demonstrate its efficiency for QM/MM MD simulations. Apart from its high performance, especially on GPUs, and a wide selection of features, OpenMM is a highly-flexible and easily-extensible program, ideal for the development of novel multiscale methods. Thanks to the open-ended design of MiMiC, the OpenMM-MiMiC interface will automatically support any new QM client program interfaced with MiMiC for QM/MM and, with minimal changes needed, new multiscale methods implemented, opening up new research directions beyond electrostatic embedding QM/MM.

Interface (matter)

10.48550/arxiv.2502.06539

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Dataset for the article "MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry"

Zenodo (CERN European Organization for Nuclear Research) (2019)

Jógvan Magnus Haugaard Olsen Viacheslav Bolnykh Simone Meloni Emiliano Ippoliti Martin P. Bircher

This dataset contains additional material related to the article: "MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry". The preprint is available at https://doi.org/10.26434/chemrxiv.7635986. Final article is available at https://doi.org/10.1021/acs.jctc.9b00093.

10.5281/zenodo.2547316

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456-S: Repeated Measurements of Binge-Drinking during Pregnancy

American Journal of Epidemiology (2005)

Katrine Albertsen Anders Nyboc Andersen Jógvan Magnus Haugaard Olsen Naja Hulvej Rod Morten Grønbæk

Binge drinking

10.1093/aje/161.supplement_1.s114c

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On the accuracy of molecular simulation-based predictions of k_offvalues: a Metadynamics study

bioRxiv (Cold Spring Harbor Laboratory) (2020)

Riccardo Capelli Wenping Lyu Viacheslav Bolnykh Simone Meloni Jógvan Magnus Haugaard Olsen

Abstract Molecular simulations have made great progresses in predicting k off values—the kinetic constant of drug unbinding, a key parameter for modern pharmacology—yet computed values under- or over-estimate experimental data in a system- and/or technique-dependent way. In an effort at gaining insights on this issue, here we used an established method to calculate k off values—frequency-adaptive metadynamics with force field— and a subsequent QM/MM descriptions of the interactions. First, using force field-based metadynamics, we calculate k off of the Positron Emission Tomography (PET) ligand iperoxo targeting the human muscarinic acetylcholine receptor M 2 . In line with previously performed in silico studies, the prediction (3.7 ± 0.7 ⋅ 10 −4 s −1 ) turned out to differ significantly from the experimentally measured value (1.0 ± 0.2 ⋅ 10 −2 s −1 ). Next, we use DFT-based QM/MM simulations to show that this discrepancy arises from erroneous force field energetics at the transition state. It turns out that this discrepancy is partly caused by lack of electronic polarization and/or charge transfer in commonly employed force field. We expect these issues to arise also in other systems where charged portions of the system play a pivotal role, such as protein- or DNA-protein complexes. Graphical TOC Entry

Metadynamics

Force Field

Millisecond

10.1101/2020.03.30.015396

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Citations (2)

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials

Journal of Chemical Theory and Computation (2015)

Jógvan Magnus Haugaard Olsen Nanna Holmgaard List Kasper Kristensen Jacob Kongsted

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

10.1021/acs.jctc.5b00078

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Citations (60)

Benchmarks and Workflow for Harmonic IR and Raman Spectra

Jonas Vester David Carrasco‐Busturia Kenneth Ruud Magnus Ringholm Jógvan Magnus Haugaard Olsen

We present a workflow, benchmarks, and applications to provide a roadmap for simulating harmonic IR and Raman spectra for large solute-solvent systems by employing a polarizable-embedding quantum-mechanics (PE-QM) approach. This multiscale modeling scheme divides the system into a central core region described by quantum-mechanical methods and an environment region described through the fragment-based polarizable embedding (PE) model. The workflow involves generating representative structures, calculating properties, and post-processing data. Benchmark calculations quantify errors introduced by some of the key approximations used in our approach and discuss its strengths and weaknesses. Finally, we apply the workflow to acetone in three different solvents, comparing simulated spectra to experimental results to further evaluate our approach and identify potential weaknesses. Accurate simulations of solute-solvent systems are an important step toward modeling more complex molecular systems with a fragment-based PE approach.

Benchmark (surveying)

Yukawa potential

Fragment (logic)

Harmonic

10.26434/chemrxiv-2024-5g38f

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