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Overcoming the Chemical Complexity Bottleneck in on-the-Fly Machine Learned Molecular Dynamics Simulations
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Improved Treatment of 1–4 Interactions in Force Fields for Molecular Dynamics Simulations
Traditional force fields commonly use a combination of bonded torsional terms and empirically scaled nonbonded interactions to capture 1-4 energies and forces of atoms separated by three bonds in a molecule. While this approach can yield accurate torsional energy barriers, it often leads to inaccurate forces and erroneous geometries and creates an interdependence between dihedral terms and nonbonded interactions, complicating parametrization and reducing transferability. Here, in this paper, we demonstrate that 1-4 interactions can be accurately modeled using only bonded coupling terms, eliminating the need for arbitrarily scaled nonbonded interactions altogether. Furthermore, by leveraging the automated parametrization capabilities of the Q-Force toolkit, we efficiently determine the necessary coupling terms without the need for manual adjustment. Our approach is first validated on a range of small molecule systems, encompassing both flexible and rigid structures, and shows a significant improvement in force field accuracy, obtaining subkcal/mol mean absolute error for every molecule tested. We further extend the bonded-only model for 1-4 interactions to Amber ff14sb, CHARMM36, and OPLS-AA force fields to reproduce ab initio gas and implicit solvent ϕ,ψ surfaces of alanine dipeptide.
Transport Properties of Liquid Pentaerythritol Tetranitrate (PETN) from Molecular Dynamics Simulations
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Implementing reactivity in molecular dynamics simulations with harmonic force fields
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Molecular dynamics simulations of a hydrophilic MIL-160-based membrane demonstrate pressure-dependent selective uptake of industrially relevant greenhouse
Oral presentation for ACS Spring Meeting
Surface hopping molecular dynamics simulation of ultrafast methyl iodide photodissociation mapped by Coulomb explosion imaging
Our simulation demonstrates the robustness of the Coulomb explosion imaging technique in studying methyl iodide photodissociation, and shows that it can be effectively used for imaging non-adiabatic transitions in coordinate space.
Data-driven molecular dynamics simulation of water isotope separation using a catalytically active ultrathin membrane
Water isotope separation, specifically separating heavy from light water, is a technologically important problem due to the usage of heavy water in applications such as nuclear magnetic resonance, nuclear power, and spectroscopy.
Understanding ionic transport in perovskite lithium-ion conductor Li 3/8 Sr 7/16 Ta 3/4 Hf 1/4 O 3 : a neutron diffraction and molecular dynamics simulation study
Solid-state Li-ion electrolytes (SSEs) are essential for the development of next-generation solid-state Li-metal batteries and new Li-extraction electrochemical cells.
Quasiclassical sampling and Wigner sampling of initial vibrational coordinates and momenta for polyatomic molecules in Monte Carlo molecular dynamics simulations
In a quasiclassical trajectory simulation, the vibrational modes are initialised with quantised vibrational energies, but vibrational phases are sampled by Monte Carlo. This requires an algorithm to assign coordinates and momenta to the various atoms. In this work, we present two methods for implementing this for nonrotating polyatomic molecules, namely, fixed-energy vibrational-state-selected initial conditions and thermal initial conditions. We also present a method for initiating classical trajectories with a ground-state Wigner distribution. These vibrational treatments are sufficient to initialise trajectories for unimolecular processes, and we also show how they can be applied to simulate bimolecular collision processes. The treatments of unimolecular and bimolecular collision processes are available in two Python codes called wigner_state_selected.py and bimolecular_collision.py, respectively, which will generate initial condition files that are recognisable by the SHARC and SHARC-MN computer programs for dynamics calculations. Both codes are available as standalone programs, as well as being included in SHARC-MN, and they will be included in future versions of SHARC. Here, the methods implemented in these codes are mostly also available in the ANT computer program, and those that are not available in ANT will be incorporated in future versions of ANT.
High-pressure phases of liquid silane studied using first-principles molecular dynamics simulations
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Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations
We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.
Trends in Ionic Liquid Diffusion in Graphite Slit Pores from Molecular Dynamics Simulation and Machine Learning
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Entrapment of Volatile Organic Compounds in Defective UiO-66 Metal-Organic-Framework: Ab Initio Molecular Dynamics Simulations at 300K
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Entrapment of VOCs in Defective UiO-66 MOF: Ab Initio Molecular Dynamics Simulations at 300K
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Using molecular dynamics simulations to validate a new approach for determining the melting curves of materials
The Los Alamos National Laboratory (LANL), located in the state of New Mexico (United States), is one of the most iconic research centers in the world. Founded in 1943 as part of the Manhattan Project, it emerged from a global conflict and an unprecedented scientific emergency. At that time, the United States feared that Nazi Germany might develop an atomic weapon first. Under the direction of physicist J. Robert Oppenheimer, the U.S. government established a secret laboratory in an isolated region of the Los Alamos plateau, bringing together some of the greatest scientific minds of the era. This site, then known as Project Y, became the birthplace of the first atomic bomb.