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LAMMPS: Yes Yes Yes Yes Yes Yes I Yes Yes Has potentials for soft and solid-state materials and coarse-grain systems Free open source, GNU GPLv2: Sandia: MacroModel: Yes Yes Yes Yes Yes No I Yes No OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimizing, MD.
The pressure value that is attempted to compute, is such that when plugged into momentum equations a divergence-free velocity field results. The mass imbalance is often also used for control of the outer loop. The name of this class of methods stems from the fact that the correction of the velocity field is computed through the pressure-field.
Most computerized databases will create a table of thermodynamic values using the values from the datafile. For MgCl 2 (c,l,g) at 1 atm pressure: Thermodynamic properties table for MgCl 2 (c,l,g), from the FREED datafile. Some values have truncated significant figures for display purposes. The table format is a common way to display ...
Lemkul et al. have used steered molecular dynamics simulations to calculate the potential of mean force to assess the stability of Alzheimer's amyloid protofibrils. [6] Gosai et al. have also used umbrella sampling simulations to show that potential of mean force decreases between thrombin and its aptamer (a protein-ligand complex) under the ...
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 .
Simcenter STAR-CCM+ is a commercial Computational Fluid Dynamics (CFD) based simulation software developed by Siemens Digital Industries Software.Simcenter STAR-CCM+ allows the modeling and analysis of a range of engineering problems involving fluid flow, heat transfer, stress, particulate flow, electromagnetics and related phenomena.
Free-energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free-energy differences from molecular dynamics or Metropolis Monte Carlo simulations.
Schematic of D2Q9 lattice vectors for 2D Lattice Boltzmann. Unlike CFD methods that solve the conservation equations of macroscopic properties (i.e., mass, momentum, and energy) numerically, LBM models the fluid consisting of fictive particles, and such particles perform consecutive propagation and collision processes over a discrete lattice.