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In recent discussions with OpenEye about free energy calculations on their Orion cloud computing platform, it became clear they will benefit from an open analysis library (`alchemlyb` in particular) b…
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The (soon-to-be-implemented) treatment for this is:
* We do not add the restraint to the fully interacting state if in explicit solvent.
* We add the restraint if in implicit solvent/vacuum.
Is t…
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I assume this problem occurs because utils.Mol2File is applied on my input, a pdb, instead of a mol2 file. Should the ligand always passed as mol2 file?
```
2016-11-22 17:11:51,492: MPI disabled.
…
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Hi, I recently used this package to generate some statistical data, it failed when some of the molecules' experiment values were not provided. Is there a solution to this kind of data?
Error:
```…
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I am running AToM for ABFE for my systems. I adapted the control script from the tutorial and I am trying it on different ligands (more than 20 heavy atoms) bound to the same protein. For some of them…
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In https://github.com/pyiron/atomistics/pull/123 the LAMMPS output for calc_static() defines the output energy as `energy`. This equals the potential energy calculated by calc_md(). We should address …
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@wxj6000 suggests to increase the density of DFT grids to (99, 590) as the default scheme, so as to align with the newest settings in Gaussian 16. Additionally, adding a different grids scheme for pos…
sunqm updated
4 months ago
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Hi,
Quaternion is very convenient for describing the orientation of a molecule (and the relative orientation of molecule A with respect to B). However, I didn't find a simple way to define quaterni…
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Right now, the SmallMoleculeProposalEngine does not correctly respect protonation states, due to code that converts the OpenMM topology to an oemol (will raise issue there).
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Let's be sure what we're asking in the modelling, before we submit a request to e.g. Bun to resolve these matters. My first shot is below. Are these the interesting questions? Are these the relevant m…