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In the file ```Cluster.py``` at line 205, there is ```energy = self.get_potential_energy()```. However, the class ```Cluster``` does not have a function named ```get_potential_energy()```
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This issue thread is intended to discuss improved restraint handling during equlibration in BioSimSpace. We currently only support backbone restraints using the `restraint_backbone` keyword, which rel…
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As the title indicates, can I use it to generate nonmetal clusters? Such as B.
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The implementation of Langevin dynamics in Faunus for a Lennard-Jones fluid/gas is well underway in my fork of Faunus. Checklist which should preferably be handled as separate PRs:
- [x] Working exam…
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**Describe the bug**
When I run
```
python -m unittest discover tests/
```
In the flarestack folder in my terminal, it throws me me errors saying there is no module named numpy, even though I ra…
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Hi,
This is for CP-SAT in the OR-Tools 7.1.6722 via Python.
The minimisation problem below can be run as is or with variable b fixed to zero. With b = 0, the solution is [0, 1, 10] with cost -1…
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I've noticed that {'maxfev':50} often results in >200 actual function evaluations. Is there a way to ensure this number is closer to what one desires, for example when the function to be evaluated is …
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It seems plausible that an SHGO variant might be capable of finding good plateaus, which is to say relatively stable local minima where there is no particularly steep dropoff nearby. I realize that is…
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The *Model basics* section (23.1) says:
> But there’s a better way to tackle that problem: a numerical minimisation tool called Newton-Raphson search. The intuition of Newton-Raphson is pretty simp…
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Hi! I thought I had this running but it's failing when it reaches the "performing inference on FOLD" stage. Here's my command and the error. Any ideas?
Contents of my INPUTS folder: b0.nii.gz /…