logmd 0.1.16

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

LogMD: View/Share MD While It Runs

Install

pip install logmd

Try with

• ase_demo.py
• openmm_demo.py
• 
• From terminal:

logmd 1crn.pdb`.

We currently support Atomic Simulation Environment (ASE) and OpenMM

vote here for other backends

Doesn't solve your problem? Let us know! Like it? Buy us a coffee!

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