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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 .
The functional form of the OPLS force field is very similar to that of AMBER: = + + += = = ([+ ()] + [ ()] + [+ ()] + [ ()]) = > (+) with the combining ...
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.
OpenKIM has been directly integrated into various prominent molecular modelling and potential fitting software including LAMMPS, [13] ASE, DL_POLY, GULP, and potfit, and is recognized in the molecular modelling community as being a critical step towards improving accessibility and reproducibility in the field.
The potential functions representing the non-bonded energy are formulated as a sum over interactions between the particles of the system. The simplest choice, employed in many popular force fields, is the "pair potential", in which the total potential energy can be calculated from the sum of energy contributions between pairs of atoms ...
Another class of machine-learned interatomic potential is the Gaussian approximation potential (GAP), [87] [88] [89] which combines compact descriptors of local atomic environments [90] with Gaussian process regression [91] to machine learn the potential energy surface of a given system.
Bond order potential is a class of empirical (analytical) interatomic potentials which is used in molecular dynamics and molecular statics simulations. Examples include the Tersoff potential , [ 1 ] the EDIP potential, the Brenner potential, [ 2 ] the Finnis–Sinclair potentials, [ 3 ] ReaxFF, [ 4 ] and the second-moment tight-binding ...
The Lennard-Jones Potential is a mathematically simple model for the interaction between a pair of atoms or molecules. [3] [4] One of the most common forms is = [() ()] where ε is the depth of the potential well, σ is the finite distance at which the inter-particle potential is zero, r is the distance between the particles.