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Figure out what to do with three clashing molecules #28

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tomnewport opened this issue Jan 31, 2016 · 0 comments
Open

Figure out what to do with three clashing molecules #28

tomnewport opened this issue Jan 31, 2016 · 0 comments
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release-0.1-alpha

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If A clashes with B, B with C and C with A then alchembed won't work. Here are some ideas:

  • Do a simple (A alchembed B) alchembed C?
    • Could be difficult, particles will wander in vacuum
    • Dummy particles to prevent diffusion?
  • Combine B and C and hope for the best?
  • Do A alchembed B then alchembed C and just don't worry about diffusion
  • Reduce cutoff distance so clash threshold is higher
@tomnewport tomnewport added this to the release-0.1-alpha milestone Jan 31, 2016
@tomnewport tomnewport self-assigned this Jan 31, 2016
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