MD Simulation

How to generate topology of small molecules & ligands for MD Simulation?

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generate topology of small molecules & ligands for MD simulation

Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation tutorials. In this article, we will explain how can you generate the topology of ligands for MD simulation of complex or small molecules only. Keep Reading

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Tutorial: MD Simulation of small organic molecules using GROMACS

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MD Simulation of small molecules

GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of small organic molecules. Keep Reading

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Tutorial: MD simulation with mixed solvents using GROMACS

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MD simulation with mixed solvents

In this tutorial, we are performing MD simulation in mixed solvents of methanol and water using GROMACS [1,2]. You can follow our previous articles for MD simulation of a simple protein and a protein-ligand complex. Keep Reading

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