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High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. [1] The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies.
But molecular dynamics simulations can explicitly model polarizability with the introduction of induced dipoles through different methods, such as Drude particles or fluctuating charges. This allows for a dynamic redistribution of charge between atoms which responds to the local chemical environment.
Also, Langevin dynamics allows temperature to be controlled as with a thermostat, thus approximating the canonical ensemble. Langevin dynamics mimics the viscous aspect of a solvent. It does not fully model an implicit solvent; specifically, the model does not account for the electrostatic screening and also not for the hydrophobic effect. For ...
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. [2] VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects.
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) [1] is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model (not to be confused with CHARMM). It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms). [2]
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids.It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide.
Coarse-grained models have found practical applications in molecular dynamics simulations. [1] Another case of interest is the simplification of a given discrete-state system, as very often descriptions of the same system at different levels of detail are possible.