Sökning: "gromacs"

Visar resultat 1 - 5 av 13 uppsatser innehållade ordet gromacs.

  1. 1. Dipole Orientation of Gas Phase Ubiquitin Using Time Dependent Electric Fields

    Kandidat-uppsats, Uppsala universitet/Molekyl- och kondenserade materiens fysik

    Författare :Harald Agelii; [2020]
    Nyckelord :dipole orientation; protein; spectography; GROMACS; simulation; single particle imaging;

    Sammanfattning : The method of dipole orientation of protein complexes using electric fields plays a key role in the development of single particle imaging, since it enables orientation of the protein in vacuum. In the orientation process the protein is exposed to an external electric field along which the dipole axis of the protein will eventually align. LÄS MER

  2. 2. Analys av Organiska Molekyler i Mikroskopiska Vattendroppar

    Kandidat-uppsats, Uppsala universitet/Molekyl- och kondenserade materiens fysik; Uppsala universitet/Molekyl- och kondenserade materiens fysik; Uppsala universitet/Molekyl- och kondenserade materiens fysik

    Författare :David Sawert; Oskar Anderhagen Holmes; Aron Johanson; [2020]
    Nyckelord :Simulering; Kraftfält; CGENFF; OPLS-AA; GAFF; CHARMM; AMBER;

    Sammanfattning : The aim of the study was to analyse where different organic molecules situated themselves in relation to the water surface of a water microdroplet and use the resulting data to compare three different forcefields in the simulation package GROMACS. The forcefields used were: General AMBER forcefield (GAFF), Optimized potentials for liquid simulations - all atoms (OPLS-AA), and CHARMM general force field (CGenFF). LÄS MER

  3. 3. Benchmarking Physical Properties of Water Models

    Kandidat-uppsats, Uppsala universitet/Molekyl- och kondenserade materiens fysik

    Författare :Tomas André; [2019]
    Nyckelord :Water Models; Molecular Dynamics; Properties of water; MD; Simulation; GROMACS;

    Sammanfattning :     Water is a fundamental part of life as we know it, and by that also a fundamental for biology, chemistry, and parts of physics. Understanding how water behaves and interacts is key in many fields of all these three branches of science. LÄS MER

  4. 4. Computational Modeling and Characterization of the Human Tri-Heteromeric GABAA Receptor

    Master-uppsats, KTH/Tillämpad fysik

    Författare :Michael Luxemburg; [2019]
    Nyckelord :;

    Sammanfattning : -aminobutyric acid receptors of type A (GABAARs) are the majorinhibitory neurotransmitter receptors in the human brain, andare modulated by a vast range of exogenous molecules, such assedatives and anesthetics. In the last year, the first cryo-electronmicroscopy (cryo-EM) images of the closed and desensitized statesof the GABAAR were released, enabling fruitful research throughsimulations of these complex proteins. LÄS MER

  5. 5. Melting points of binary and ternary eutectic chloride salts : MD simulations on LiCl-NaCl-KCl and its binary constituents

    Uppsats för yrkesexamina på avancerad nivå,

    Författare :André Larsson Sihm; [2019]
    Nyckelord :Liquid metal battery; molecular dynamics; simulation; eutectic; salt;

    Sammanfattning : This thesis investigates how well the Alexandria (WBK) force-field can predict themelting point for multi-cation chloride salts with molecular dynamic (MD) simulationsin Gromacs 4.6.7. Researched is the eutectic ternary salt LiCl-NaCl-KCl(53. LÄS MER