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It might be a good idea to add the possibility to run SENPAI with simulation parameters loaded from an external file.
This would for example ease running the same simulation on multiple files in seq…
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Thanks for this nice module!
I am trying to use the [QDpi Model](https://gitlab.com/RutgersLBSR/qdpi), for running a MD simulation describing the whole waterbox with the NNP, following this [commen…
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@peastman : I'm curious about the origin of the [`DrudeLangevinIntegrator`](https://github.com/pandegroup/openmm/blob/master/plugins/drude/openmmapi/include/openmm/DrudeLangevinIntegrator.h#L41-L50). …
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## Is your feature request related to a problem? ##
In molecular dynamics simulations, users frequently have to inspect energy-like terms such as potential or kinetic energy, temperature, or pressure…
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This paper https://dissem.in/p/102408039/structure-and-dynamics-of-water-confined-in-imogolite-nanotubes exists as an open access version in preprint server chemRxiv: https://doi.org/10.26434/chemrxiv…
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**Submitting author:** @degiacom (Matteo Degiacomi)
**Repository:** https://github.com/CCPBioSim/BioSim-analysis-workshop
**Branch with paper.md** (empty if default branch):
**Version:** v1.0
**Edito…
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I saw the article "Protocols for Multi-Scale Molecular Dynamics Simulations in Amber and Gromacs: a Case Study of Intrinsically Disordered Amyloid Beta" from biorxiv. I want to use your method to repr…
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Would it make sense to have this be part of the interface? If so, we would need to be able to dispatch on boundary condition types, which might require rejiggering the type parameters of `AbstractSyst…
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**Meeting Zoom link:** https://ucl.zoom.us/j/99880132263
**Topic:** Nsp13 Monthly Meeting UCL/UNC/Astex.
**Time:** Apr 4, 2022 05:00 PM London (BST), UNC 12:00 noon.
**Chair:** Tom Knight
…
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### What is the title of the roadmap you are submitting?
Roadmap to Bioinformatics
### Roadmap Link
# Bioinformatics Roadmap
**0. Why Bioinformatics?**
- **What is Bioinformatics?** Bioinfo…