Gromacs
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Cited in
(only showing first 100 items - show all)- A comparison of generalized hybrid Monte Carlo methods with and without momentum flip
- IMD
- sGDML
- AMBER
- MPICH-G2
- OOMPAA
- GSHMC
- GAMESS
- NAMD
- TINKER
- Protein interaction network analysis -- approach for potential drug target identification in \textit{Mycobacterium tuberculosis}
- A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization
- WebMO
- B-spline tight frame based force matching method
- A novel method for calculating relative free energy of similar molecules in two environments
- Single channel quantum color image encryption algorithm based on HSI model and quantum Fourier transform
- Exploration of synthetic multifunctional amides as new therapeutic agents for Alzheimer's disease through enzyme inhibition, chemoinformatic properties, molecular docking and dynamic simulation insights
- \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
- Normal mode dynamics of voltage-gated \(\mathrm{K}^+\) channels: gating principle, opening mechanism, and inhibition
- 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
- Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand
- APBS
- LAMMPS
- CHARMM
- PLUMED
- CPMD
- DESMOND
- MCELL
- ESPResSo
- AdResS
- ZIBgridfree
- A modified amino acid network model contains similar and dissimilar weight
- A coarse graining method for the dimension reduction of the state space of biomolecules
- Coarse grained molecular dynamics and theoretical studies of carbon nanotubes entering cell membrane
- Combining stochastic and deterministic approaches within high efficiency molecular simulations
- PNFFT
- A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
- PFC3D
- Macrodox
- GROMOS
- Dimensionality reduction of complex metastable systems via kernel embeddings of transition manifolds
- Molecular dynamics simulation of heat transfer and stresses in thin films caused by a short laser pulse
- BioShape
- GANM
- AFMPB
- LINCS
- FFTSVD
- DL_POLY
- DL_POLY_3
- Cellware
- Data-driven molecular modeling with the generalized Langevin equation
- 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
- Spectral gap of replica exchange Langevin diffusion on mixture distributions
- NAMD2
- AutoDock Vina
- PyMOL
- Physics-informed distribution transformers via molecular dynamics and deep neural networks
- Molecular dynamics simulations of the full-length prion protein
- Molecular dynamics study of the fibril elongation of the prion protein fragment PrP106-126
- FMM-Yukawa
- QUESO
- GROWL
- ZIBMolPy
- ProtoMol
- Chimera
- Qmd-plot
- A comparative molecular dynamics-phase-field modeling approach to brittle fracture
- The mechanism of pulsed electric field (PEF) targeting location on the spatial conformation of pine nut peptide
- Numerical aspect of large-scale electronic state calculation for flexible device material
- Molecular dynamics. With deterministic and stochastic numerical methods
- Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation
- Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors
- Wavelets as basis functions to represent the coarse-graining potential in multiscale coarse graining approach
- A semi-analytical approach to molecular dynamics
- 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
- Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia
- Landmark diffusion maps (L-dMaps): accelerated manifold learning out-of-sample extension
- VADAR
- GANM: A protein-ligand docking approach based on genetic algorithm and normal modes
- Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics
- Salinas
- Why does \(\beta \)-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies
- Generator estimation of Markov jump processes
- SpAMM
- sPuReMD
- SETTLE
- An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics
- Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis
- Heme peroxidase clothing and inhibition with polyphenolic substances revealed by molecular modeling
- X-PLOR
- Guided motion of short carbon nanotube driven by non-uniform electric field
- An analysis of wavelet frame based scattered data reconstruction
- 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
- Using piecewise polynomials for faster potential function evaluation
- OVITO
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