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It's very early days, but the Molecular Dynamics Database ([MDDB](https://mddbr.eu/about/)) is starting to do some very initial hosting of datasets. (https://mmb.mddbr.eu/#/browse)
I don't suppose …
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### 🎮 Game Request
Verlet integration is a numerical method used to integrate Newton’s equations of motion. It is frequently used to calculate trajectories of particles in molecular dynamics simula…
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**Submitting author:** @armcdona (Ashley Ringer McDonald)
**Repository:** https://github.com/calpolyccg/MDSAPT
**Branch with paper.md** (empty if default branch): JOSS_Pub
**Version:** v2.0
**Editor:*…
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## New Use Case
Aspect | Detail
------------ | -------------
Summary | C1997 (Platforms providing web-access to molecular level tools for guiding systems level modelling)
Usecase Group | Molec…
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## New Use Case
Aspect | Detail
------------ | -------------
Summary | C1997 (Platforms providing web-access to molecular level tools for guiding systems level modelling)
Usecase Group | Molec…
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- MDFP (https://pubs.acs.org/doi/10.1021/acs.jcim.6b00778), a package for extracting features from molecular dynamics trajectories, which can be used for machine learning applications.
- LigGrep (htt…
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Hello
I understand that most PDB files do not contain hydrogens hence NGL connects the heavy atoms and labels it as a hydrogen bond. Would it be possible to tell NGL to display correct hydrogen bon…
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Right now, generating a movie is restricted to the animation tool (e.g., requires trajectories).
It would be great if we could move the animation code to a general class:
- movies of vibrations
-…
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**Submitting author:** @gezelter (J. Daniel Gezelter)
**Repository:** https://github.com/OpenMD/OpenMD/
**Branch with paper.md** (empty if default branch):
**Version:** v3.1
**Editor:** @srmnitc
**Re…
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I'm currently working with fingerprints calculation in molecular dynamics trajectories.
To do this I need to convert protein and ligand in a pdb file for every single frame, and then reopen every fil…