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Bilayer building #39

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2 of 21 tasks
ctk3b opened this issue Nov 25, 2014 · 1 comment
Closed
2 of 21 tasks

Bilayer building #39

ctk3b opened this issue Nov 25, 2014 · 1 comment

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@ctk3b
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ctk3b commented Nov 25, 2014

Input parameters:

  • Fractions of lipids, e.g.: [(lipid_A, 0.3), (lipid_B, 0.7)]
  • Specify number of lipids and figure out box dimensions
  • Various arrangements
    • random
    • patterned
    • phase separated
  • spacing between layers
    • how do we provide the reference atom?
    • could assume that provided lipids are always oriented with head-groups up in the z-direction
  • area per lipid
  • solvent
    • height of solvent
    • lipid to solvent ratio
    • height of full box
  • flag mirror bottom and top layer or not

Performance issues:

  • solvation
    • benchmark for bottlenecks
    • accelerate our code
    • can we intelligently wrap genbox? (or wait for the python api to come out)
  • local energy minimization
    • write to gromacs/hoomd/lammps, run, read coordinates back in
@tcmoore3 tcmoore3 mentioned this issue Nov 26, 2014
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@ctk3b
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ctk3b commented Dec 1, 2014

Re-opening under @tcmoore3 tcmoore3

@ctk3b ctk3b closed this as completed Dec 1, 2014
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