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We should install `packmol` during the travis-ci scripts to facilitate testing of this (optional) feature.
Perhaps there's a way for us to make it a conda package?
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Currently we have a mismatch where we have some details about how solvation happens in the SolvationSettings and some in SolventComponent.
My proposal is that **anything that defines the molecular …
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Currently, the function `utils.smiles_to_mdtraj_ffxml` is nonfunctional as it calls on a function `convert_molecule(pdb_filename, mol2_filename)` which is undefined. I don't see this function anywhere…
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I'm getting these warning, wrongly, in VSCode:
One may try to see if that happens wi…
lmiq updated
6 months ago
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https://github.com/zincware/IPSuite/blob/9dca6052a6350710a5d7505729e7ce3ec34474f7/ipsuite/base/base.py#L92
`data_id` typically is either first or last configuration. The current way of having a def…
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**Bug summary**
If you try to **insert zero molecules of a species**, PACKMOL is grumpy. Example:
```python
# Use 1000 total ions
n_ions = 1000
x_li = job.sp.conc
# Taken fro…
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where are the 2-3 most computationally-intensive loops in the fortran code that could be parallelized using OPENMP ?
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The problem is that `gmx solvate` can put waters inside the hydrophobic environment. There are multiple ways to overcome the issue. One would be to get read of all waters that have fewer than a certai…
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```
import ipsuite as ips
project = ips.Project(automatic_node_names=True)
mapping = ips.geometry.BarycenterMapping(data=None)
# Define the CP2K calculations
cp2k = ips.calculators.CP2KSing…
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@slochower shared the following script with me, which seems to touch on some very useful areas.
We should polish in into a full-fledged example!
Some complications toward making this into an exa…