Top Tweets for #MDtraj
When I started to analyze the #MDtrajectories, I put all I needed to learn (for me) and make accessible (for others) into #mdciao (using the powerful #mdtraj under the hood).
Though it has some #GPCR & #Gproteinspecific stuff, give it a spin for your analysis pipelines!
[7/n]
Molecular Dynamics for beginners using Gromacs. How about running all the MD steps including data analysis on 1 Jupyter Notebook with Python libraries & wrappers @ProjectJupyter @GMX_TWEET @orbeckst @github #NGLView #MDtraj #pytraj
plz share your feedback
https://t.co/5h3rzYJUTM
@macports @condaforge Select atoms with #mdtraj or @mdanalysis. Use ATOMS={@ mdt:{protein and (backbone or resname ALA)}}
or ATOMS={@ mda:{resid 3:5}
The big issue for #MDtraj is sustainability:
- one maintainer, unfunded, working on tools unsuitable within DESRES (the current employer)
- "long tail of small packages" -- when issues get tagged by a stale not...
#staletale
#MDtraj was created because @rmcgibbo didn't know how to use other people tools and hence, created his own -- in retrospect, it doesn't seem like the best idea #standardproliferation
#TTClust is now on #conda!
You can easily install it with "conda install -c tubiana -c conda-forge ttclust" ๐
https://t.co/4h9nnhdDAg
#MDTraj #Python #MolecularDynamics #Clustering
If anyone cared here's a slightly more in-depth mol2 emoji parser evaluation for today's TIL:
Fields tested: reading only (if possible), atom label, type and residue name.
@mdanalysis works.
#mdtraj throws a KeyError if there's an emoji for the atom type.
@julienmich80 Only one I tested, but it looks like @mdanalysis somehow handles mol2 emojis ๐ (note: this was not comprehensive test).
As results emerge from our projects in #molecularDynamics I am enjoying and learning a lot developing Tauren-MD (https://t.co/vhq9AF5Dy7). Now it has a @ZENODO_ORG DOI for its releases ๐ฅณ. Thanks to @mdanalysis and #MDTraj for such nice libraries. #structuralbiology #proteins
@mdanalysis and #MDTraj again get an honorable mention at #SDMS18 in the context of file format support and ease of use/access
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