NAMD

swMATH3198MaRDI QIDQ15731FDOQ15731

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Official website: http://www.ks.uiuc.edu/Research/namd/

Cited In (88)

• 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
• Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
• High performance computing in multiscale problems of gas dynamics
• Metadynamics study of mutant human interferon-gamma forms
• Fractal and complex network analyses of protein molecular dynamics
• TNAMD: Implementation of \texttt{TIGER2} in NAMD
• Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx
• FFT, FMM, or multigrid? A comparative study of state-of-the-art Poisson solvers for uniform and nonuniform grids in the unit cube
• A short note on the fast evaluation of dihedral angle potentials and their derivatives
• Parallel molecular dynamics with irregular domain decomposition
• Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling
• Title not available (Why is that?)
• Title not available (Why is that?)
• Understanding the influence of structural hierarchy and its coupling with chemical environment on the strength of idealized tropocollagen-hydroxyapatite biomaterials
• Spectral accuracy in fast Ewald-based methods for particle simulations
• SpECTRE: A task-based discontinuous Galerkin code for relativistic astrophysics
• Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations
• Progress in developing Poisson-Boltzmann equation solvers
• The GROMACS and NAMD software packages comparison.
• A special purpose array processor architecture for the molecular dynamics simulation of point-mutated proteins
• Title not available (Why is that?)
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• Efficient implementation of the many-body reactive bond order (REBO) potential on GPU
• 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
• NAMD2: Greater scalability for parallel molecular dynamics
• Quantum dot-DNA interaction: Computational issues and preliminary insights on use of quantum dots as biosensors
• A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
• A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure
• A hydrophobicity study on wavy and orthogonal textured surfaces
• Hierarchical modeling of diffusive transport through nanochannels by coupling molecular dynamics with finite element method
• ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models
• IMD
• TNPACK
• AMBER
• Algorithmic challenges in computational molecular biophysics
• OOMPAA
• ToSCA
• CHARMM
• PLUMED
• AFMPB
• FFTSVD
• NAMD2
• TNAMD
• SETTLE
• OpenUH
• MACI
• sPuReMD
• Interconnection networks for parallel molecular dynamics simulation based on Hamiltonian cubic symmetric topology
• General purpose molecular dynamics simulations fully implemented on graphics processing units
• MMM2D
• Apbsmem
• ChaNGa
• OpenAtom
• RASPA
• QHDFoam
• Statistical mechanical theory of protein folding in water environment
• A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma
• Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
• Monte Carlo simulation of biomolecular systems with BIOMCSIM
• Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
• PetFMM -- a dynamically load-balancing parallel fast multipole library
• Numerical simulation of the motion of granular material using object-oriented techniques
• A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements
• Monitoring energy drift with shadow Hamiltonians
• TrpAQP: computer simulations to determine the selectivity of aquaporins
• Parallelization of a level set method for simulating dendritic growth
• Molecular systems with open boundaries: theory and simulation
• Active learning for saddle point calculation
• Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein
• Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations
• On theoretical upper limits for valid timesteps of implicit ODE methods
• Title not available (Why is that?)
• 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
• Using the method of weighted residuals to compute potentials of mean force
• Molecular dynamics study of the interaction of a shock wave with a biological membrane
• 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
• Solvers for \(\mathcal{O}(N)\) electronic structure in the strong scaling limit
• Bone remodelling in \textsc{BioShape}
• Microstructure-dependent dynamic fracture analyses of trabecular bone based on nascent bone atomistic simulations
• DelPhi
• Using computational approaches to study dengue virus capsid assembly
• A linear assignment approach for the least-squares protein morphing problem
• Title not available (Why is that?)
• MOLECULAR DYNAMICS SIMULATIONS OF DMPC/DPPC MIXED BILAYERS

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