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I haven't profiled this but it's a fairly simple script building a topology for 200k atoms and then reading in positions from a .pdb file (generated by packmol). Chews up ~11GB to build the topology.
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ctk3b updated
9 years ago
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Seems like there are two issues: 1) packmol isn't installed properly and 2) there's a permission issue when attempting to write a .mol2 file in the tests.
https://ci.appveyor.com/project/ctk3b/mbuild…
ctk3b updated
9 years ago
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Currently, the default size box generated by `packmol.pack_box` is deliberately _extremely_ conservative (probably the resulting volume is about 8 times larger than strictly necessary in most cases) r…
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Ideally, we would have a unified pipeline which allows water to be specified as a component in much the same way as any other solute/solvent. For example, we might imagine being able to ask for:
```
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Currently the default box sizes used by `openmoltools.packmol.pack_box` are too large, requiring substantially longer equilibration. Reduce the initial box size to something still generous but not qui…
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After running
conda config --add channels http://conda.binstar.org/omnia
conda install openmoltools
And running
nosetests openmoltools -v --exe
I got:
ERROR: Failure: ImportError (No module na…
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It kind of feels like the `packmol` stuff doesn't belong here.
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I think I know how to do this now, so this is just a reminder for me to do this.
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For context see #3
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Things to investigate:
- [ ] wrapper around genbox for both the solvate and solvent_box functions
- [ ] look into Cython or equivalent acceleration for functions
- [x] wrapper around packmol
ctk3b updated
9 years ago