NAMD

swMATH3198MaRDI QIDQ15731

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Related Items (66)

Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx ⋮ On theoretical upper limits for valid timesteps of implicit ODE methods ⋮ Unnamed Item ⋮ Unnamed Item ⋮ Monte Carlo simulation of biomolecular systems with BIOMCSIM ⋮ Unnamed Item ⋮ Unnamed Item ⋮ Unnamed Item ⋮ Numerical simulation of the motion of granular material using object-oriented techniques ⋮ Using the method of weighted residuals to compute potentials of mean force ⋮ A molecular dynamics study of wenzel state water droplets on anisotropic surfaces ⋮ A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces ⋮ A hydrophobicity study on wavy and orthogonal textured surfaces ⋮ Solvers for $\mathcal{O} (N)$ Electronic Structure in the Strong Scaling Limit ⋮ Parallelization of a level set method for simulating dendritic growth ⋮ New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics ⋮ Physics-informed distribution transformers via molecular dynamics and deep neural networks ⋮ Molecular systems with open boundaries: theory and simulation ⋮ Unnamed Item ⋮ Using computational approaches to study dengue virus capsid assembly ⋮ A coarse graining method for the dimension reduction of the state space of biomolecules ⋮ Parallel Molecular Dynamics with Irregular Domain Decomposition ⋮ A Parallel Multiscale Simulation Toolbox for Coupling Molecular Dynamics and Finite Elements ⋮ SpECTRE: A task-based discontinuous Galerkin code for relativistic astrophysics ⋮ Microstructure-dependent dynamic fracture analyses of trabecular bone based on nascent bone atomistic simulations ⋮ A short note on the fast evaluation of dihedral angle potentials and their derivatives ⋮ Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns ⋮ Spectral accuracy in fast Ewald-based methods for particle simulations ⋮ Molecular dynamics study of the interaction of a shock wave with a biological membrane ⋮ A linear assignment approach for the least-squares protein morphing problem ⋮ A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure ⋮ A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver ⋮ General purpose molecular dynamics simulations fully implemented on graphics processing units ⋮ A special purpose array processor architecture for the molecular dynamics simulation of point-mutated proteins ⋮ Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins ⋮ Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein ⋮ High performance computing in multiscale problems of gas dynamics ⋮ TrpAQP: Computer Simulations to Determine the Selectivity of Aquaporins ⋮ Bone Remodelling in BioShape ⋮ PetFMM-A dynamically load-balancing parallel fast multipole library ⋮ Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations ⋮ Metadynamics study of mutant human interferon-gamma forms ⋮ Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization ⋮ Eucb: a C++ program for molecular dynamics trajectory analysis ⋮ TNAMD: Implementation of \texttt{TIGER2} in NAMD ⋮ Hierarchical modeling of diffusive transport through nanochannels by coupling molecular dynamics with finite element method ⋮ Monitoring energy drift with shadow Hamiltonians ⋮ Understanding the influence of structural hierarchy and its coupling with chemical environment on the strength of idealized tropocollagen-hydroxyapatite biomaterials ⋮ Fractal and complex network analyses of protein molecular dynamics ⋮ Efficient implementation of the many-body reactive bond order (REBO) potential on GPU ⋮ Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations ⋮ A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma ⋮ Unnamed Item ⋮ Milp-hyperbox classification for structure-based drug design in the discovery of small molecule inhibitors of SIRTUIN6 ⋮ Petri nets formalism facilitates analysis of complex biomolecular structural data ⋮ Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling ⋮ Quantum dot-DNA interaction: Computational issues and preliminary insights on use of quantum dots as biosensors ⋮ FFT, FMM, or Multigrid? A comparative Study of State-Of-the-Art Poisson Solvers for Uniform and Nonuniform Grids in the Unit Cube ⋮ Interconnection networks for parallel molecular dynamics simulation based on Hamiltonian cubic symmetric topology ⋮ ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models ⋮ Statistical Mechanical Theory of Protein Folding in Water Environment ⋮ Algorithmic challenges in computational molecular biophysics ⋮ NAMD2: Greater scalability for parallel molecular dynamics ⋮ MOLECULAR DYNAMICS SIMULATIONS OF DMPC/DPPC MIXED BILAYERS ⋮ Progress in developing Poisson-Boltzmann equation solvers ⋮ Active learning for saddle point calculation

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