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Molecular Dynamics Simulation programs calculate the potential energy of the system each frame in trajectory, but what I want is how much of each residual share in all potential energy? So, i am wonde…
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**Submitting author:** @flokno (Florian Knoop)
**Repository:** https://gitlab.com/vibes-developers/vibes
**Version:** v1.0.2
**Editor:** @jgostick
**Reviewers:** @keipertk, @ajjackson
**Archive:**…
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## Idea
I want to formalize the format for storing HDF5 Trajectories on disk, and provide some kind of a "contract" that our code can say that it implements. It makes sense for the writers of traject…
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**Submitting author:** @valeriewelborn (Valerie Vaissier)
**Repository:** https://github.com/WelbornGroup/ELECTRIC
**Version:** v1.0.0
**Editor:** @richardjgowers
**Reviewers:** @amandadumi, @govarguz…
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**Story:** *As a* molecular dynamics user, *I want* to set up MDAnalysis quickly and easily, *so that* I can move onto further analysis.
**Story:** *As a* molecular dynamics user, *I want* to conve…
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I have a very weird segmentation fault in one of my simulations. The curios thing is that I do multiple simulations in exactly the same manner and the only thing I change between different simulations…
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The following sequence of calls throws an exception:
```
paging = LinkedData::Models::Class.in(self).include(:unmapped).aggregate(:count, :children).page(page, size)
results = paging.page(1, size).…
mdorf updated
4 years ago
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**Describe the bug**
I have adapted the "1_cyclohexane_1_ethanol" start-up python code and use it on other molecules.
One molecule is rosiglitazone (drug-like), whose net charge = 0, and the adapted…
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@ChrisRackauckas pointed out a paper (https://arxiv.org/abs/1912.03253) that uses the Calvo and Sanz-Sara methods in HMC. These integrators are already implemented in DiffEq (https://docs.juliadiffeq.…