Streaming trajectories from a simulation engine with IMDv3

Configuring the simulation engine for IMDv3

To stream a trajectory from a simulation engine that supports IMDv3, first use the appropriate input options on the simulation engine to prepare it for the IMDClient receiver.

Below, we have proided brief instructions on how to setup the various simulation engine to output stream data using IMDv3.

GROMACS

In GROMACS, you can use gmx mdrun with the -imdwait flag to ensure that GROMACS will wait for a client before starting the simulation. In GROMACS, you will know that the simulation is ready and waiting for the MDAnalysis IMDReader client when this line is printed to the terminal:

IMD: Will wait until I have a connection and IMD_GO orders.

You are now ready to connect to the simulation engine with a client.

NAMD

To use IMDv3 with NAMD, add the following lines to your NAMD configuration file:

IMDon yes
IMDport <port, must be the same port used for the client>
IMDwait <yes/no>
IMDfreq <frequency of sending data to the client>

IMDsendPositions <yes/no>
IMDsendEnergies <yes/no>
IMDsendTime <yes/no>
IMDsendBoxDimensions <yes/no>
IMDsendVelocities <yes/no>
IMDsendForces <yes/no>
IMDwrapPositions <yes/no>

Once the simulation is ready for a client connection, it will print following terminal message:

Info: INTERACTIVE MD AWAITING CONNECTION

You are now ready to connect to the simulation engine with a client.

LAMMPS

To use IMDv3 with LAMMPS, add the following lines to your LAMMPS input script:

fix ID group-ID imd <port> trate <frequency> version 3 unwrap <on/off> time <on/off> box <on/off> coordinates <on/off> velocities <on/off> forces <on/off>

Once the simulation is ready for a client connection, it will print following terminal message:

Waiting for IMD connection on port <port>

You are now ready to connect to the simulation engine with a client.

Using IMDClient with MDAnalysis

Once the simulation is ready for a client connection, setup your MDAnalysis Universe like this:

from IMDClient.IMD import IMDReader
import MDAnalysis as mda
# Pass host and port of the listening simulation
# engine as the trajectory argument

# GROMACS
u = mda.Universe("topology.gro", "imd://localhost:8888")
# NAMD
u = mda.Universe("topology.psf", "imd://localhost:8888")

While this package allows the IMDReader to be automatically selected based on the trajectory URL matching the pattern ‘imd://<host>:<port>’, the format can be explicitly selected by passing the keyword argument ‘format=”IMD”’ to the Universe.