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  2. Molecular dynamics - Wikipedia

    en.wikipedia.org/wiki/Molecular_dynamics

    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.

  3. Comparison of software for molecular mechanics modeling

    en.wikipedia.org/wiki/Comparison_of_software_for...

    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 ...

  4. Metadynamics - Wikipedia

    en.wikipedia.org/wiki/Metadynamics

    In 2015, White, Dama, and Voth introduced experiment-directed metadynamics, a method that allows for shaping molecular dynamics simulations to match a desired free energy surface. This technique guides the simulation towards conformations that align with experimental data, enhancing our understanding of complex molecular systems and their behavior.

  5. Molecular modelling - Wikipedia

    en.wikipedia.org/wiki/Molecular_modelling

    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.

  6. Force field (chemistry) - Wikipedia

    en.wikipedia.org/wiki/Force_field_(chemistry)

    GROMOS (GROningen MOlecular Simulation) – a force field that comes as part of the GROMOS software, a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. [72] GROMOS force field A-version has been developed for application to aqueous or apolar solutions of proteins, nucleotides, and sugars.

  7. Langevin dynamics - Wikipedia

    en.wikipedia.org/wiki/Langevin_dynamics

    A real world molecular system is unlikely to be present in vacuum. Jostling of solvent or air molecules causes friction, and the occasional high velocity collision will perturb the system. Langevin dynamics attempts to extend molecular dynamics to allow for these effects.

  8. Car–Parrinello molecular dynamics - Wikipedia

    en.wikipedia.org/wiki/Car–Parrinello_molecular...

    The Car–Parrinello method is a type of molecular dynamics, usually employing periodic boundary conditions, planewave basis sets, and density functional theory, proposed by Roberto Car and Michele Parrinello in 1985 while working at SISSA, [1] who were subsequently awarded the Dirac Medal by ICTP in 2009.

  9. LAMMPS - Wikipedia

    en.wikipedia.org/wiki/LAMMPS

    Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. [1] LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software , distributed under the terms of the GNU General Public License .