NAMD
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Software:15731
swMATH3198MaRDI QIDQ15731FDOQ15731
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Cited In (66)
- Bone Remodelling in BioShape
- 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
- Title not available (Why is that?)
- MOLECULAR DYNAMICS SIMULATIONS OF DMPC/DPPC MIXED BILAYERS
- Solvers for $\mathcal{O} (N)$ Electronic Structure in the Strong Scaling Limit
- Molecular systems with open boundaries: theory and simulation
- Statistical Mechanical Theory of Protein Folding in Water Environment
- Active learning for saddle point calculation
- 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
- High performance computing in multiscale problems of gas dynamics
- Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein
- 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
- PetFMM-A dynamically load-balancing parallel fast multipole library
- Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling
- A Parallel Multiscale Simulation Toolbox for Coupling Molecular Dynamics and Finite Elements
- 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
- Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations
- On theoretical upper limits for valid timesteps of implicit ODE methods
- 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
- TrpAQP: Computer Simulations to Determine the Selectivity of Aquaporins
- 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
- Algorithmic challenges in computational molecular biophysics
- Interconnection networks for parallel molecular dynamics simulation based on Hamiltonian cubic symmetric topology
- General purpose molecular dynamics simulations fully implemented on graphics processing units
- 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
- Microstructure-dependent dynamic fracture analyses of trabecular bone based on nascent bone atomistic simulations
- Parallel Molecular Dynamics with Irregular Domain Decomposition
- Title not available (Why is that?)
- Using computational approaches to study dengue virus capsid assembly
- 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
- A linear assignment approach for the least-squares protein morphing problem
- Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
- Numerical simulation of the motion of granular material using object-oriented techniques
- Monitoring energy drift with shadow Hamiltonians
- Parallelization of a level set method for simulating dendritic growth
- Title not available (Why is that?)
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