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Concept

Comparison of software for molecular mechanics modeling

Résumé

This is a list of computer programs that are predominantly used for molecular mechanics calculations.

Source officielle

https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling

À propos de ce résultat

Cette page est générée automatiquement et peut contenir des informations qui ne sont pas correctes, complètes, à jour ou pertinentes par rapport à votre recherche. Il en va de même pour toutes les autres pages de ce site. Veillez à vérifier les informations auprès des sources officielles de l'EPFL.

Proximité ontologique

Chimie

Chimie numérique: Chimie numérique

Cours associés (4)

BIO-315: Structural biology

The main focus of this course is on the molecular interactions defining the structure, dynamics and function of biological systems. The principal experimental and computational techniques used in stru

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Introduction to molecular dynamics and Monte-Carlo simulation methods.

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The aim of the course is to provide a chemical understanding and intuition to decipher and predict chemical processes in living systems.

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Séances de cours associées (32)

Simulations de dynamique moléculaire

Explore les surfaces d'énergie potentielles dans les simulations de dynamique moléculaire et l'utilisation de méthodes mécaniques quantiques / moléculaires mixtes.

Dynamique moléculaire et Monte Carlo

Couvre les méthodes de calcul des systèmes moléculaires à température finie, en mettant l'accent sur l'échantillonnage stochastique et les simulations d'évolution du temps.

Simulations de pliage des protéines

Couvre la théorie et les applications pratiques des simulations de pliage de protéines en utilisant la dynamique moléculaire, en se concentrant sur les effets des solvants et l'analyse de la dynamique de pliage.

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Publications associées (33)

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

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Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

The exploration of electronically excited states and the study of diverse photochemical and photophysical processes are the main goals of molecular electronic spectroscopy. Exact quantum-mechanical simulation of such experiments is, however, beyond current ...

EPFL2024

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Personnes associées (3)

Ursula Röthlisberger, Ivano Tavernelli, Jiri Vanicek

Concepts associés (21)

Molecule editor

A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages.

Parallel tempering

Parallel tempering, in physics and statistics, is a computer simulation method typically used to find the lowest energy state of a system of many interacting particles. It addresses the problem that at high temperatures, one may have a stable state different from low temperature, whereas simulations at low temperatures may become "stuck" in a metastable state. It does this by using the fact that the high temperature simulation may visit states typical of both stable and metastable low temperature states.

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

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MOOCs associés (2)

Path Integral Methods in Atomistic Modelling

The course provides an introduction to the use of path integral methods in atomistic simulations. The path integral formalism allows to introduce quantum mechanical effects on the equilibrium and (ap

Path Integral Methods in Atomistic Modelling

The course provides an introduction to the use of path integral methods in atomistic simulations. The path integral formalism allows to introduce quantum mechanical effects on the equilibrium and (ap