End-to-end distance between atoms? about openmm HOT 2 OPEN

You can do something like this to print out the current distance:

positions = simulation.context.getState(getPositions=True).getPositions()
print(norm(positions[94]-positions[67]))

If you want to record it periodically during the simulation you might do something like

distances = []
for i in range(n):
    simulation.step(1000)
    positions = simulation.context.getState(getPositions=True).getPositions()
    distances.append(norm(positions[94]-positions[67]).value_in_unit(nanometers))

Another option is that you just record your whole trajectory to a DCD or XTC file. Then you can use a tool like MDTraj or MDAnalysis to analyze it later and extract the distances.

from openmm.

@peastman thanks for the super quick response!

I'll play around with this over the weekend and see where I get and then post a reproducible example here for anyone else who might be interested in this for the future, and then close this issue.

from openmm.