MD Simulation

Tutorial: A quick MD simulation using NAMD and VMD

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Molecular dynamics (MD) simulation has become an important methodology in research covering systems consisting of millions of atoms. We have provided several articles on MD simulation including the GROMACS [1] installation and performing MD. In this article, we will learn about “QwikMD” a plugin in NAMD [3], and VMD [4]. Keep Reading

Tutorial: MD simulation output analysis of protein using GROMACS

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Molecular dynamics (MD) simulation is an important step in studying the dynamics of macromolecules. In one of the previous articles, MD simulation of chain A of insulin (PDB ID: 1ZNI) was performed using GROMACS. The output analysis of that simulation is explained in this article. Keep Reading

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