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We should be using the [Chapman-Kolmogorov validation](http://www.emma-project.org/latest/api/generated/pyemma.msm.ChapmanKolmogorovValidator.html#pyemma.msm.ChapmanKolmogorovValidator) on our final M…
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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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Are there examples of CJSON with multiple conformers / coordinate sets?
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The authors addressed most of my minor concerns but failed to address my major critique simply because they do not know how to produce a molecular dynamics (MD) trajectory for testing. It is in within…
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I re-implemented AdLaLa integrator by Tiffany and Ben (https://github.com/TiffanyVlaar/ThermodynamicParameterizationOfNNs/blob/master/AdLaLa.ipynb) here:
https://github.com/choderalab/pinot/blob/ma…
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**Submitting author:** @micahgale (Micah D. Gale)
**Repository:** https://github.com/idaholab/MontePy
**Branch with paper.md** (empty if default branch): joss_submit
**Version:** v0.2.7
**Editor:** Pe…
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Hello there,
For a current project, I need to be able to import thousands of molecules and control them (Empties are welcome for that matter) according to a simulation a scientist provided me with.
…
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**Submitting author:** @IonRepo (Claudio Cazorla)
**Repository:** https://github.com/IonRepo/IonDiff
**Branch with paper.md** (empty if default branch): main
**Version:** 1.6
**Editor:** @rkurchin
**R…
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I have modified the test [simulation](https://github.com/openmm/openmm-torch/blob/master/tutorials/openmm-torch-nnpops.ipynb) of alanine dipeptide for a box of TIP3P water using the ANI1ccx model. I w…
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The implementation of `angle_style cosine/periodic` in LAMMPS contains an undocumented factor of 2, which means that lammps_interface leads to angle bending constants which are too large for UFF and o…
acroy updated
3 years ago