A few examples to ease out your lives

  • NAMD
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    NAMD has a quite didactic user manual with sample scripts for running the simulations. Here, I assemble them all and provide a slight deviation from the usual process.
  • Packmol
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    A noob's guide on using the ubiquitous software Packmol. A sample system is created consisting of cis-fullerene, drug and water. There are no prerequisites for trying out this tutorial.
  • Towhee
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    This page will guide you through the basics of Monte Carlo Simulations and how to implement it using the Towhee code. Towhee is an open source code and works remarkably well for phase equilibria studies.
  • NanoChannel
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    A guide on how to create a channel or portal using Graphene sheets and Carbon Nanotubes, for performing steered Molecular Dynamics. The example covers the use of VMD and Packmol for achieving the task.
  • Gold NP's
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    Simple tutorial to help you create Gold Nanoparticles using the open source tool OpenMD. Insights on how to control the size of the particle and the geometry is also provided.