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In the Computational Materials Science: An Introduction by June Lee, he discusses molecular dynamics and density functional theory with examples from LAMMPS and QuantumEspresso, and explains LAMMPS and QuantumEspresso in detail.

I was wondering if there is a similar text in Computational Biology for molecular dynamics but in GROMACS/NAMD, I can use tutorials but I would like to find a textbook with more examples and explanations.

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    $\begingroup$ This might fit better on the new Matter Modeling SE. It focuses more specifically on molecular and material simulation, so you might find someone there who knows some MD. Or you may find an existing question with a suitable reference. $\endgroup$ – Tyberius Sep 18 '20 at 21:16
  • $\begingroup$ @Tyberius, thank you so much. I posted it there too. $\endgroup$ – Josh Sep 19 '20 at 2:48

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