arXiv subjects

Jógvan Magnus Haugaard Olsen

Publications and source records attributed to Jógvan Magnus Haugaard Olsen.

9 recordsLinked to original sources

arXiv2025

Atom-centered electric multipole moments dynamically generated from QM/MM MD simulations

Atom-centered electric multipole moments can be extremely useful in chemistry as they enable the systematic mapping of a complex electrostatic problem to a simpler model. However, since they do not correspond to physical observables, there is no unique way to define them. In this work, we present an extension of the dynamically generated RESP charges (D-RESP) method, referred to as xDRESP, where atom-centered multipoles are computed from mixed quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. We compare the ability of xDRESP charges to reproduce the electrostatic potential, as well as molecular multipoles, against the performance of fixed point-charge models commonly used in force fields. Moreover, we highlight cases where DRESP atomic multipoles can provide valuable information about chemical systems, such as indicating when polarization plays a significant role, and chemical reactions, in which xDRESP atomic multipoles can be used as an on-the-fly analysis tool to track changes in electron density.

physics.chem-ph↗

arXiv2025

Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More

MiMiC is a framework for modeling large-scale chemical processes that require treatment at multiple resolutions. It does not aim to implement single-handedly all methods required to treat individual subsystems, but instead, it relegates this task to specialized computational chemistry software while it serves as an intermediary between these external programs, and computes the interactions between the subsystems. MiMiC minimizes issues typically associated with molecular dynamics performed with multiple programs, by adopting a multiple-program multiple-data paradigm combined with a loose-coupling model. In this article, we present the addition of a new client program, CP2K, to the MiMiC ecosystem, which required a major refactoring of the entire framework and in the end allowed us to unlock its full flexibility. By thorough timing analysis, we verify that the introduced changes do not affect the performance of MiMiC or CP2K, and neither are they a source of significant computational overheads that would be detrimental to simulation efficiency. Moreover, we demonstrate the benefits of the framework's modular design, by performing a QM/MM MD simulation combining CP2K with previously interfaced OpenMM, with no additional implementation effort required.

physics.chem-ph↗

arXiv2025

OpenMM-MiMiC Interface for Efficient and Flexible Multiscale Simulations

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.

physics.chem-ph↗

arXiv2024

MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding QM/MM that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

physics.chem-ph↗

arXiv2024

Multiscale Biomolecular Simulations in the Exascale Era

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes. However, leveraging the immense computational power of exascale computing requires innovative algorithms and software designs. In this context, we discuss the current status and future prospects of multiscale biomolecular simulations on exascale supercomputers with a focus on QM/MM MD. We highlight our own efforts in developing a versatile and high-performance multiscale simulation framework with the aim of efficient utilization of state-of-the-art supercomputers. We showcase its application in uncovering complex biological mechanisms and its potential for leveraging exascale computing.

physics.bio-ph↗

arXiv2021

Wavefunction-based electrostatic-embedding QM/MM using CFOUR through MiMiC

We present an interface of the wavefunction-based quantum-chemical software CFOUR to the multiscale modeling framework MiMiC. Electrostatic embedding of the quantummechanical (QM) part is achieved by analytic evaluation of one-electron integrals in CFOUR, while the rest of the QM/MM operations are treated according to the previous MiMiC-based QM/MM implementation. Long-range electrostatic interactions are treated by a multipole expansion of the potential from the QM electron density to reduce the computational cost without loss of accuracy. Testing on model water/water systems, we verified that the CFOUR interface to MiMiC is robust, guaranteeing fast convergence of the SCF cycles and optimal conservation of the energy during the integration of the equations of motion. Finally, we verified that the CFOUR interface to MiMiC is compatible with the use of a QM/QM multiple time-step algorithm, which effectively reduces the cost of AIMD or QM/MM-MD simulations using higher level wavefunction-based approaches compared to cheaper density-functional theory based ones. The new wavefunction-based AIMD and QM/MM-MD implementation was tested and validated for a large number of wavefunction approaches, including Hartree-Fock and post-Hartree-Fock methods like Moller-Plesset, coupled cluster, and complete active space self-consistent field.

physics.chem-ph↗

arXiv2020

The DIRAC code for relativistic molecular calculations

DIRAC is a freely distributed general-purpose program system for 1-, 2- and 4-component relativistic molecular calculations at the level of Hartree--Fock, Kohn--Sham (including range-separated theory), multiconfigurational self-consistent-field, multireference configuration interaction, coupled cluster and electron propagator theory. At the self-consistent-field level a highly original scheme, based on quaternion algebra, is implemented for the treatment of both spatial and time reversal symmetry. DIRAC features a very general module for the calculation of molecular properties that to a large extent may be defined by the user and further analyzed through a powerful visualization module. It allows the inclusion of environmental effects through three different classes of increasingly sophisticated embedding approaches: the implicit solvation polarizable continuum model, the explicit polarizable embedding, and frozen density embedding models. DIRAC was one of the earliest codes for relativistic molecular calculations and remains a reference in its field.

physics.chem-ph↗

arXiv2018

Response properties of embedded molecules through the polarizable embedding model

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 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 consider in order to obtain trustworthy results in an efficient manner. To lower the threshold for new users wanting to explore the use of the PE model, we describe and discuss important aspects related to its practical use. This includes directions on how to generate input files and how to run a calculation.

physics.chem-ph↗

arXiv2017

Modeling the absorption spectrum of the permanganate ion in vacuum and in aqueous solution

The absorption spectrum of the MnO$_{4}$$^{-}$ ion has been a test-bed for quantum-chemical methods over the last decades. Its correct description requires highly-correlated multiconfigurational methods, which are incompatible with the inclusion of finite-temperature and solvent effects due to their high computational demands. Therefore, implicit solvent models are usually employed. Here we show that implicit solvent models are not sufficiently accurate to model the solvent shift of MnO$_{4}$$^{-}$, and we analyze the origins of their failure. We obtain the correct solvent shift for MnO$_{4}$$^{-}$ in aqueous solution by employing the polarizable embedding (PE) model combined with a range-separated complete active space short-range density functional theory method (CAS-srDFT). Finite-temperature effects are taken into account by averaging over structures obtained from ab initio molecular dynamics simulations. The explicit treatment of finite-temperature and solvent effects facilitates the interpretation of the bands in the low-energy region of the MnO$_{4}$$^{-}$ absorption spectrum, whose assignment has been elusive.

physics.chem-ph↗