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        <title>MD Theory Series - Series - Compchems</title>
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        <description>MD Theory Series - Series - Compchems</description>
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    <title>An Introduction to Enhanced Sampling and Metadynamics</title>
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    <pubDate>Sat, 18 May 2024 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[An Introduction to Enhanced Sampling with a focus on Metadynamics simulations]]></description>
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    <title>Thermostats in Molecular Dynamics</title>
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    <pubDate>Thu, 28 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[Learn about the different types of thermostats used in Molecular Dynamics simulations and how they control temperature in this comprehensive guide. Understand the pros and cons of each thermostat and how to implement them in your simulation using GROMACS]]></description>
</item><item>
    <title>Molecular Dynamics: Equations of motion</title>
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    <pubDate>Wed, 27 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[Dive deep into the fundamental principles of Molecular Dynamics with this guide on equations of motion. Learn the mathematical description of motion in MD simulations, the types of integrators used, and the role of forces in biomolecular simulation. ]]></description>
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    <title>Molecular Dynamics: Periodic Boundary Conditions (PBC)</title>
    <link>/molecular-dynamics-periodic-boundary-conditions-pbc/</link>
    <pubDate>Tue, 26 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[In this article, I will show you the reasons behind the implementation of the so-called Periodic Boundary Conditions (PBC), a key topic in the computational simulation of molecular structures. ]]></description>
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    <title>Barostats in Molecular Dynamics</title>
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    <pubDate>Mon, 25 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[Learn about the different types of barostats used in Molecular Dynamics simulations and how they control pressure in this comprehensive guide. Understand the pros and cons of each barostat, its implementation in biomolecular simulation using GROMACS and the impacts of pressure on biomolecular systems. ]]></description>
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    <title>Molecular Dynamics (MD)</title>
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    <pubDate>Mon, 25 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[Learn about the basics of Molecular Dynamics (MD) simulations, the underlying principles and the key concepts required to run a simulation of biomolecular systems in this comprehensive guide. Explore the applications and limitations of MD, the software options available and how to get started with MD simulations ]]></description>
</item><item>
    <title>Molecular Dynamics: Ensembles</title>
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    <pubDate>Mon, 25 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[Gain a deeper understanding of Ensembles used in Molecular Dynamics (MD) simulations with this comprehensive guide. Learn about the various ensembles such as NVE, NVT, NPT and their application in MD simulations. Understand how they impact the thermodynamic properties of the biomolecular system, and how to implement them in your MD simulation using GROMACS.]]></description>
</item><item>
    <title>Setting up a Molecular Dynamics simulation</title>
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    <pubDate>Mon, 25 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[Setting up a realistic simulation of a given molecular system involves different steps some of which depend on its complexity, and on the conditions we choose for our experiment. In this article, I try to explain to you which are the typical steps to perform in Molecular Dynamics (MD). However, always keep in mind that an MD simulation protocol is highly system-dependent, and each system needs to be analyzed differently.]]></description>
</item><item>
    <title>Force Fields in Molecular Dynamics</title>
    <link>/force-fields-in-molecular-dynamics/</link>
    <pubDate>Sat, 23 Jul 2022 00:00:00 &#43;0000</pubDate><author>
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    <description><![CDATA[A Force Field is a set of functional terms and parameters required to compute the potential energy equation of a molecular system. Different force fields are nowadays available. It is extremely important to know the limitations and capabilities of each one of them. ]]></description>
</item><item>
    <title>Molecular Dynamics: Bonded interactions</title>
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    <pubDate>Sat, 23 Jul 2022 00:00:00 &#43;0000</pubDate><author>
        <name>false</name>
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    <description><![CDATA[Bonded interactions are one of the two components building the Molecular Mechanics potential energy equation. Here you can find a detailed explanation of the various contributions to the bonding interactions and their importance in molecular modeling.  ]]></description>
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