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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 Lennard-Jones potential is a simple model that still manages to describe the essential features of interactions between simple atoms and molecules: Two interacting particles repel each other at very close distance, attract each other at moderate distance, and eventually stop interacting at infinite distance, as shown in the Figure.
The functional form of the OPLS force field is very similar to that of AMBER: = + + += = = ([+ ()] + [ ()] + [+ ()] + [ ()]) = > (+) with the combining ...
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 ...
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.
In a simulation, the potential energy of an atom, , is given by [3] = (()) + (), where is the distance between atoms and , is a pair-wise potential function, is the contribution to the electron charge density from atom of type at the location of atom , and is an embedding function that represents the energy required to place atom of type into the electron cloud.
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 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.