imd

Python operations available from the imd module, used to display and interact with a molecule in a molecular dynamics simulation.

• connect(host, port): Connect to a simulation running on host host and listening for incoming connections on port port.

• pause(): If connected, cause the simulation to pause.

• detach(): If connected, detach from the simulation. The simulation will continue to run, but no more frames will be received until a connection is re-established.

• kill(): If connected, terminate the simulation. The connection will also be abolished.

• transfer(rate): Set/get how often the remote simulation sends coordinate frames to VMD. If rate is omitted or is negative, no action is taken and the current value is returned. A value of 1 corresponds to every frame being sent; a value of 2 corresponds to every other frame, etc.

• keep(rate): Set/get how often received coordinates frames are kept by VMD as part of an animation. If rate is omitted or is negative, no action is taken and the current value is returned. A value of 0 means no frames are saved. A value of 1 corresponds to every frame being saved; a value of 2 corresponds to every other frame, etc.

• copyunitcell(True/False): Control how unitcell information is passed to the new frame that recieved via IMD. If set to False (the default) unit cell information would be taken from the IMD connection. Since the IMD protocol currently has no provisions for communicating the unit cell information, the unit cell dimensions are set to zero. If set to True the cell information is copied from the previous frame.
  WARNING: when using imd.copyunitcell(True) with simulations in the NPT ensemble, the resulting unitcell information will be incorrect.