SimStream Example: Simulating Alanine Dipeptide

This example runs a simulation of the small molecule Alanine Dipeptide and streams logs and RMSD. RMSD is a metric for judging how similar two molecular states are for the same model.

Instructions

Installing OpenMM

The easiest way to install OpenMM is to use the Anaconda distribution of Python and run conda install -c https://conda.anaconda.org/omnia openmm

If you do not wish to use Anaconda, install OpenMM from source by following the instructions in the OpenMM docs

Start the Logfile Consumer

1. Open a terminal
2. cd path/to/simstream/examples/openmm_example
3. python openmm_log_consumer.py

Start the RMSD Consumer

1. Open a terminal
2. cd path/to/simstream/examples/openmm_example
3. python openmm_rmsd_consumer.py

Starting the Producer

1. Open a new terminal
2. cd path/to/simstream/examples/openmm_example
3. python openmm_streamer.py application/sim.out application/trajectory.dcd application/input.pdb application/input.pdb

Starting the Simulation

1. Open a new terminal
2. cd path/to/simstream/examples/openmm_example/application
3. python alanine_dipeptide.py > sim.out

The Logfile Consumer should now be printing tagged log entries to the screen; the RMSD Consumer should be printing the calculated RMSD each time the trajectory file is written.