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Tanya Faltens

Request for more instructions and explanation

This pre-made demonstration and learning simulation is a great idea.

It would be really helpful to augment the instructions with some explanations of what to do _after_ hitting “simulate”. For example, can you explain the best viewing options and what other features of VMD we should try? Can you point out some useful things that we should be able to see in the simulation?

  1. nanoBIO tools
  2. tool:partsub
  3. Visual Molecular Dynamics (VMD)

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    AbderRahman N Sobh

    Hi,

    Thanks for your question, sorry this response is a little late! The previous version of the tool was more of a placeholder for the newly-released plugin that we have been working on for some time. The point of the previous setup was to simply guide a user through what it looks like for a surface + linker + DNA to be opened up in VMD, in other words it was a preview of what we envisioned our tool would allow users to create. Currently, users can now build the entire system themselves and run it in NAMD all inside of a single session. Please see the "Supporting Docs" for a detailed tutorial on how to use the new tool's many features.

    Thanks,

    AbderRahman (Abby) Sobh

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