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Dear OpenMM community,
We (the Riniker lab @rinikerlab and the Hünenberger lab @csms-ethz at ETH Zurich) have developed a shifted reaction-field (RF) correction (https://doi.org/10.1039/D0CP03835K…
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(1) Outgoing radiation assuming no aerosol
rlutaf, rlutcsaf, rsutaf: need a standard names. Current names do not include aerosol free component.
- rlut, rlutaf: toa_outgoing_longwave_flux
- rlutc…
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We could then use this class to document methods like ``tfep.app.TFEPMapBase.configure_flow()``.
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Hello,
I am a little confused about the definitions of rho_m and rho_r in background.c and perturbations.c
I understand that for components behaving like matter and radiation, they need to be in…
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There are various free energy methods that utilize scaling of intermolecular interactions. For example one can compute the chemical potential by inserting an additional particle/molecule into the syst…
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I've had a quick shot at running ABFEs with SOMD2. The overall experience was a massive step up from SOMD! The recent sire documentation was also super clear and comprehensive. However, I've had a cou…
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Currently we only support relative free energy calculations but absolute solvation free energy calculations are routinely carried out in the field with well described protocols.
@lohedges @ppxasjs…
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Hello! I'm currently matching and merging molecules for MCL1 ligands. The basic code used to replicate these is:
```python
# ligands
lig0 = "lig_27"
lig1 = "lig_42"
# options
prematch = {}
ri…
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```
Using a MORPH file in explicit solvent with no actual changes in parameters
(initial=final).
python debug.py 0.0 1; python debug.py 0.1 1; python debug.py 0.2 1; python
debug.py 0.3 1; python…
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```
Using a MORPH file in explicit solvent with no actual changes in parameters
(initial=final).
python debug.py 0.0 1; python debug.py 0.1 1; python debug.py 0.2 1; python
debug.py 0.3 1; python…