logmd 0.1.13

Log MD trajectories with `dyn.attach(LogMd()(atoms)).

LogMD: View/Share MD While It Runs

Try in Google Colab:

Install

pip install logmd

Try with demo.py, this colab or from terminal >logmd 1crn.pdb.

We currently only support Atomic Simulation Environment (ASE) - vote here for other backends

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Use-cases

We built logmd for the two use-cases below. If there's a use-case we're missing, let's chat!

Case 1:

Inspect/share trajectory while simulation runs - just click/share the link logmd prints.

from logmd import LogMD
logmd = LogMD(num_workers=2)
dyn.attach(lambda: logmd(atoms), interval=4)
dyn.run(steps)

Case 2:

Document/visualize fixing of pdb before running simulation. Example: I want to simulate '1crn.pdb' but need to add missing residues, hydrogens, water, pH and so on. To document everything, I run logmd watch 1crn.pdb which stores all versions of 1crn.pdb as a trajectory.

>logmd watch 1crn.pdb # from terminal