P3MaZe merges P3M electrostatics with MaZe constrained dynamics to solve the long-range Poisson equation via holonomic constraints on an auxiliary mesh field, matching reference methods on NaCl and SPC/Fw while using fewer multigrid iterations.
SoftwareX1-2, 19–25 (2015)
15 Pith papers cite this work, alongside 26,815 external citations. Polarity classification is still indexing.
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representative citing papers
Causal analysis of water MD simulations shows translational motions drive orientational dynamics in supercooled HDL but remain decoupled at ambient conditions, revealing an emergent arrow of time in fluctuation couplings.
2D water-alcohol mixtures stay fully miscible with micro-segregation that grows with alcohol chain length, driven by water self-aggregation but limited by rim contacts, due to reorganization of fluctuations under charge ordering.
ColPackAgent integrates a custom colpack Python package wrapping HOOMD-blue with MCP tools and an agent skill to enable reliable autonomous workflows for colloidal packing simulations across interactive, prompt-driven, and autoresearch modes.
LSI and ζ best distinguish temperature-dependent local structure in supercooled TIP4P/2005 water under a unified neural temperature-classification benchmark, with H-bond network descriptors next.
PepMorph generates morphology-targeted peptides via a Transformer conditional VAE and reports 83% success under CG-MD validation.
A kinetic model integrating bulk, surface, and defect nucleation pathways, with rates from MD simulations, predicts that nanoscopic hydrophobic defects dominate cavitation and that bulk nucleation requires defect-free hydrophilic surfaces at around -100 MPa.
An analytical model for GPU power identifies architecture- and workload-dependent transition frequencies beyond which energy efficiency degrades, based on benchmarks on A40/A100/H100/H200 GPUs.
DeltaDiff is a physics-guided inference method that predicts mutant protein structures from a baseline diffusion model without retraining, tested on three systems with nonlocal changes.
Integrates DMR middleware into GROMACS for dynamic MPI process adaptation in molecular dynamics simulations and evaluates node-hour savings on MareNostrum 5 for bursty workloads.
SALMON 2.3 implements divide-and-conquer DFT ground-state initialization with orbital reconstruction, achieving linear scaling and enabling real-time TDDFT on systems up to 4134 atoms.
A putative homotrimeric structure of BP180 is predicted with Boltz-2 and shown to remain mostly folded over 500 ns MD trajectories, with a stiff NC16A domain and flexible Col-15.
CovAngelo implements a QM/QM/MM embedding model using quantum-information metrics to compute reaction energy profiles and barriers for covalent drug binding at lower cost than conventional methods, demonstrated on zanubrutinib to BTK.
GPU offload on the tested system yields 4-12x throughput and up to 15x energy-efficiency gains over CPU-only execution for gromacs, lammps, OpenGadget3, AthenaK and dealii-X, with gains sensitive to problem granularity.
QM/MM simulations find that Glu-to-Asp mutation raises the catalytic barrier in CviUPO while Cys-to-His lowers it but may shift the enzyme toward peroxidase behavior.
citing papers explorer
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P3MaZe: a Mass-Zero constrained-dynamics formulation of particle-mesh electrostatics
P3MaZe merges P3M electrostatics with MaZe constrained dynamics to solve the long-range Poisson equation via holonomic constraints on an auxiliary mesh field, matching reference methods on NaCl and SPC/Fw while using fewer multigrid iterations.
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Causality in Liquid Water as a Hallmark of Emergent Glassy Dynamics
Causal analysis of water MD simulations shows translational motions drive orientational dynamics in supercooled HDL but remain decoupled at ambient conditions, revealing an emergent arrow of time in fluctuation couplings.
-
Aqueous-alcohol mixtures in dimension two: miscibility and micro-segregation
2D water-alcohol mixtures stay fully miscible with micro-segregation that grows with alcohol chain length, driven by water self-aggregation but limited by rim contacts, due to reorganization of fluctuations under charge ordering.
-
ColPackAgent: Agent-Skill-Guided Hard-Particle Monte Carlo Workflows for Colloidal Packing
ColPackAgent integrates a custom colpack Python package wrapping HOOMD-blue with MCP tools and an agent skill to enable reliable autonomous workflows for colloidal packing simulations across interactive, prompt-driven, and autoresearch modes.
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Machine learning evaluation of structural descriptors for supercooled water
LSI and ζ best distinguish temperature-dependent local structure in supercooled TIP4P/2005 water under a unified neural temperature-classification benchmark, with H-bond network descriptors next.
-
Morphology-Aware Peptide Discovery via Masked Conditional Generative Modeling
PepMorph generates morphology-targeted peptides via a Transformer conditional VAE and reports 83% success under CG-MD validation.
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Water cavitation results from the kinetic competition of bulk, surface and surface-defect nucleation events
A kinetic model integrating bulk, surface, and defect nucleation pathways, with rates from MD simulations, predicts that nanoscopic hydrophobic defects dominate cavitation and that bulk nucleation requires defect-free hydrophilic surfaces at around -100 MPa.
-
Modeling and Chasing the Energy-Efficiency Sweet Spots in Modern GPUs
An analytical model for GPU power identifies architecture- and workload-dependent transition frequencies beyond which energy efficiency degrades, based on benchmarks on A40/A100/H100/H200 GPUs.
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DeltaDiff: Training-Free, Physics-Guided Machine Learning for Predicting Mutant Protein Structures
DeltaDiff is a physics-guided inference method that predicts mutant protein structures from a baseline diffusion model without retraining, tested on three systems with nonlocal changes.
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Malleable Molecular Dynamics Simulations with GROMACS and DMR
Integrates DMR middleware into GROMACS for dynamic MPI process adaptation in molecular dynamics simulations and evaluates node-hour savings on MareNostrum 5 for bursty workloads.
-
SALMON 2.3: Implementation of divide-and-conquer ground-state initialization for large-scale real-time TDDFT
SALMON 2.3 implements divide-and-conquer DFT ground-state initialization with orbital reconstruction, achieving linear scaling and enabling real-time TDDFT on systems up to 4134 atoms.
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A putative, computationally stable structure of homotrimeric BP180/collagen XVII
A putative homotrimeric structure of BP180 is predicted with Boltz-2 and shown to remain mostly folded over 500 ns MD trajectories, with a stiff NC16A domain and flexible Col-15.
-
CovAngelo: A hybrid quantum-classical computing platform for accurate and scalable drug discovery
CovAngelo implements a QM/QM/MM embedding model using quantum-information metrics to compute reaction energy profiles and barriers for covalent drug binding at lower cost than conventional methods, demonstrated on zanubrutinib to BTK.
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Node-Level Performance and Energy Characterization of Flagship Science Applications on SuperMUC-NG Phase 2
GPU offload on the tested system yields 4-12x throughput and up to 15x energy-efficiency gains over CPU-only execution for gromacs, lammps, OpenGadget3, AthenaK and dealii-X, with gains sensitive to problem granularity.
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Computationally guided modifications of CviUPO to improve catalytic activity
QM/MM simulations find that Glu-to-Asp mutation raises the catalytic barrier in CviUPO while Cys-to-His lowers it but may shift the enzyme toward peroxidase behavior.