Examples of NAMD simulations, execution and analysis.
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MD_nanoparticle: Files corresponding to a simple model of a 2 nm nanoparticle (atoms modelled as LJ potentials with parameters corresponding to gold)
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protein: Files corresponding to an example simulation of the human ubiquitin protein (PDB code: 1UBQ) generated from experimental data
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nanotube: Files corresponding to the simulation of water flow across a carbon nanotube
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membrane: A bilayer membrane made with DPPC phospholipid hydrated with TIP3P water
For an overview about preparing NAMD simulations and document describing how to execute NAMD: https://saco.csic.es/index.php/s/iyZYfPgqJEgFR2T
For an overview about analyzing results from MD simulations https://saco.csic.es/index.php/s/kps5jW3S3f3o7tr
For practical considerations about MD simulations see: https://computecanada.github.io/molmodsim-md-theory-lesson-novice/