Concept

Abalone (molecular mechanics)

Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field.

Official source

https://en.wikipedia.org/wiki/Abalone_(molecular_mechanics)

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Related concepts (7)

Comparison of force-field implementations

This is a table of notable computer programs implementing molecular mechanics force fields.

Molecular design software

Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g

Water model

In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.

Abalone (molecular mechanics) - Wikipedia

Official source

https://en.wikipedia.org/wiki/Abalone_(molecular_mechanics)

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Explores Ring Polymer Molecular Dynamics and Centroid Molecular Dynamics, approximating observables and correlations from quantum mechanics.

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Hamiltonian-Reservoir Replica Exchange and Machine Learning Potentials for Computational Organic Chemistry

Anne-Clémence Corminboeuf, Alberto Fabrizio, Benjamin André René Meyer, Raimon Fabregat I De Aguilar-Amat, Daniel Hollas

This work combines a machine learning potential energy function with a modular enhanced sampling scheme to obtain statistically converged thermodynamical properties of flexible medium-size organic molecules at high ab initio level. We offer a modular envir ...

AMER CHEMICAL SOC2020

Absolute band alignment at semiconductor-water interfaces using explicit and implicit descriptions for liquid water

Alfredo Pasquarello, Nicola Marzari, Francesco Ambrosio, Oliviero Andreussi, Zhendong Guo

Quantum mechanical simulations that include the effects of the liquid environment are highly relevant for the characterization of solid-liquid interfaces, which is crucial for the design of a wide range of devices. In this work we present a rigorous and sy ...

2019

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

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We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ab ...

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Related concepts (7)

Comparison of force-field implementations

This is a table of notable computer programs implementing molecular mechanics force fields.

Molecular design software

Water model