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Molecular dynamics simulations are often used to study biophysical systems. Depicted here is a 100 ps simulation of water. A simplified description of the standard molecular dynamics simulation algorithm, when a predictor-corrector-type integrator is used.
Constraint algorithms are often applied to molecular dynamics simulations. Although such simulations are sometimes performed using internal coordinates that automatically satisfy the bond-length, bond-angle and torsion-angle constraints, simulations may also be performed using explicit or implicit constraint forces for these three constraints.
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 ...
Multi-particle collision dynamics (MPC), also known as stochastic rotation dynamics (SRD), [1] is a particle-based mesoscale simulation technique for complex fluids which fully incorporates thermal fluctuations and hydrodynamic interactions. [2] Coupling of embedded particles to the coarse-grained solvent is achieved through molecular dynamics. [3]
IOP Publishing (previously Institute of Physics Publishing) is the publishing company of the Institute of Physics.It provides publications through which scientific research is distributed worldwide, including journals, community websites, magazines, conference proceedings and books.
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 .
The difference is that this approach relies on equilibrium statistical mechanics rather than molecular dynamics. Instead of trying to reproduce the dynamics of a system, it generates states according to appropriate Boltzmann distribution. Thus, it is the application of the Metropolis Monte Carlo simulation to molecular systems.
Materials Studio is software for simulating and modeling materials. It is developed and distributed by BIOVIA (formerly Accelrys), a firm specializing in research software for computational chemistry, bioinformatics, cheminformatics, molecular dynamics simulation, and quantum mechanics.