Gromacs

swMATH4128WikidataQ905302 ScholiaQ905302MaRDI QIDQ16313FDOQ16313

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Source code repository: https://github.com/ElsevierSoftwareX/SOFTX-D-15-00003

Cited In (only showing first 100 items - show all)

• Combining stochastic and deterministic approaches within high efficiency molecular simulations
• Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization
• High-performance large-scale atomistic simulation of thin films deposition
• Normal mode dynamics of voltage-gated \(\mathrm{K}^+\) channels: gating principle, opening mechanism, and inhibition
• Molecular dynamics simulations of the full-length prion protein
• Molecular dynamics study of the fibril elongation of the prion protein fragment PrP106-126
• Metadynamics study of mutant human interferon-gamma forms
• Reactive molecular dynamics: numerical methods and algorithmic techniques
• Orientations of special water dipoles that accelerate water molecules exiting from carbon nanotube
• A short note on the fast evaluation of dihedral angle potentials and their derivatives
• Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
• Nose-Hoover thermostat length effect on thermal conductivity of single wall carbon nanotubes
• Analyzing effects of naturally occurring missense mutations
• Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interac\-tion
• Spectral accuracy in fast Ewald-based methods for particle simulations
• A semi-analytical approach to molecular dynamics
• A Meshless Discretization Method for Markov State Models Applied to Explicit Water Peptide Folding Simulations
• Progress in developing Poisson-Boltzmann equation solvers
• A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization
• Protein interaction network analysis -- approach for potential drug target identification in \textit{Mycobacterium tuberculosis}
• Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations
• Zonal methods for the parallel execution of range-limited \(N\)-body simulations
• Efficient implementation of the many-body reactive bond order (REBO) potential on GPU
• Coupled Navier-Stokes-Molecular dynamics simulations using a multi-physics flow simulation framework
• B-spline tight frame based force matching method
• Molecular dynamics. With deterministic and stochastic numerical methods
• A boundary element formulation of protein electrostatics with explicit ions
• Massively parallel Monte Carlo for many-particle simulations on GPUs
• The interlayer shear effect on graphene multilayer resonators
• Molecular dynamics simulation of heat transfer and stresses in thin films caused by a short laser pulse
• Title not available (Why is that?)
• Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis
• Molecular dynamics simulation of peeling a DNA molecule on substrate
• Stochastic and delayed stochastic models of gene expression and regulation
• A sparse Markov chain approximation of LQ-type stochastic control problems.
• ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models
• Nanoscale thermodynamics of biological interfacial tension
• Wavelets as basis functions to represent the coarse-graining potential in multiscale coarse graining approach
• Alya: computational solid mechanics for supercomputers
• General purpose molecular dynamics simulations fully implemented on graphics processing units
• \textsf{ZIBgridfree}: efficient conformational analysis by partition-of-unity coupling
• A reference implementation of the adaptive resolution scheme in \texttt{ESPResSo}
• An analysis of wavelet frame based scattered data reconstruction
• An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics
• A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: theory and application to microfilaments
• Title not available (Why is that?)
• \(\Pi\)4U: a high performance computing framework for Bayesian uncertainty quantification of complex models
• Coarse‐grained molecular dynamics modeling of DNA–carbon nanotube complexes
• A novel method for calculating relative free energy of similar molecules in two environments
• Implementing molecular dynamics on hybrid high performance computers-short range forces
• Dimensionality reduction of complex metastable systems via kernel embeddings of transition manifolds
• Generator estimation of Markov jump processes
• A comparison of generalized hybrid Monte Carlo methods with and without momentum flip
• Physical modeling of aqueous solvation
• Entropy-based wavelet de-noising method for time series analysis
• Single channel quantum color image encryption algorithm based on HSI model and quantum Fourier transform
• Molecular dynamics of dewetting of ultra-thin water films on solid substrate
• Exploration of synthetic multifunctional amides as new therapeutic agents for Alzheimer's disease through enzyme inhibition, chemoinformatic properties, molecular docking and dynamic simulation insights
• A comparative molecular dynamics-phase-field modeling approach to brittle fracture
• Title not available (Why is that?)
• \textit{In silico} analysis of \textit{plasmodium falciparum} CDPK5 protein through molecular modeling, docking and dynamics
• Insights into the interaction of key biofilm proteins in \textit{Pseudomonas aeruginosa} PAO1 with TiO\(_2\) nanoparticle: an \textit{in silico} analysis
• Automated parameterization of intermolecular pair potentials using global optimization techniques
• A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
• Classical investigation of long-range coherence in biological systems
• Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors
• An Automatic Adaptive Importance Sampling Algorithm for Molecular Dynamics in Reaction Coordinates
• A Random Batch Ewald Method for Particle Systems with Coulomb Interactions
• Numerical aspect of large-scale electronic state calculation for flexible device material
• GANM: A protein-ligand docking approach based on genetic algorithm and normal modes
• Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach
• Generalized Fickian approach for phase separating fluid mixtures in smoothed particle hydrodynamics
• Why does \(\beta \)-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies
• Molecular Dynamics Performance Evaluation with Modern Computer Architecture
• Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation
• Length scale effect on the buckling behavior of a graphene sheets using modified couple stress theory and molecular dynamics method
• A hybrid lattice Boltzmann-molecular dynamics-immersed boundary method model for the simulation of composite foams
• Molecular modeling, simulation and virtual screening of ribosomal phosphoprotein P1 from \textit{Plasmodium falciparum}
• Molecular modeling and molecular dynamics simulations of GPI 14 in \textit{Leishmania major}: insight into the catalytic site for active site directed drug design
• Bone Remodelling in BioShape
• Numerical Modelling of Ion Transport in 5-HT3 Serotonin Receptor Using Molecular Dynamics
• Title not available (Why is that?)
• A theoretical framework for the biophysics of tubulins
• Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
• Using piecewise polynomials for faster potential function evaluation
• Petri nets formalism facilitates analysis of complex biomolecular structural data
• Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand
• A modified amino acid network model contains similar and dissimilar weight
• Spectral gap of replica exchange Langevin diffusion on mixture distributions
• Landmark diffusion maps (L-dMaps): accelerated manifold learning out-of-sample extension
• A coarse graining method for the dimension reduction of the state space of biomolecules
• Physics-informed distribution transformers via molecular dynamics and deep neural networks
• Heme peroxidase clothing and inhibition with polyphenolic substances revealed by molecular modeling
• Coarse grained molecular dynamics and theoretical studies of carbon nanotubes entering cell membrane
• Guided motion of short carbon nanotube driven by non-uniform electric field
• Computing committors in collective variables via Mahalanobis diffusion maps
• Connecting the Dots: Numerical Randomized Hamiltonian Monte Carlo with State-Dependent Event Rates
• A generalized Newton iteration for computing the solution of the inverse Henderson problem
• Mechanics of water pore formation in lipid membrane under electric field
• Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: insights from molecular dynamics simulation

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