Interactive Molecular Dynamics (IMD)

NAMD now works directly with IMD-compatible clients, such as VMD and MDAnalysis [49,61], to allow you to view and interactively steer your simulation. With IMD enabled, you can connect to NAMD at any time during the simulation to view the current state of the system or perform interactive steering. For more information about using IMD version 3 (IMDv3) with a python package IMDClient that utilizes MDAnalysis, please refer to https://imdclient.readthedocs.io/en/latest/usage.html#namd. The IMDv3 implementation in NAMD was contributed by Amruthesh Thirumalaiswamy and Lawson Woods from the MDAnalysis community.

The following options are available as a part of NAMD's IMD implementation:

• IMDon $<$ is IMD active? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not to listen for an IMD connection.

• IMDversion $<$ IMD version number $>$
  Acceptable Values: 2 or 3
  Default Value: 2
  Description: Specifies the version of IMD protocol used. Currently VMD uses 2 and IMDClient (MDAnalysis) uses 3. The detailed version 3 protocol can be found https://imdclient.readthedocs.io/en/latest/protocol_v3.htmlhere.

• IMDport $<$ port number to expect a connection on $>$
  Acceptable Values: positive integer
  Description: This is a free port number on the machine that node 0 is running on. This number will have to be entered into VMD.

• IMDfreq $<$ timesteps between sending coordinates $>$
  Acceptable Values: positive integer
  Description: This allows coordinates to be sent less often, which may increase NAMD performance or be necessary due to a slow network.

• IMDwait $<$ wait for an IMD connection? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: If no, NAMD will proceed with calculations whether a connection is present or not. If yes, NAMD will pause at startup until a connection is made, and pause when the connection is lost.

• IMDignore $<$ ignore interactive steering forces $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: If yes, NAMD will ignore any steering forces generated by VMD to allow a simulation to be monitored without the possibility of perturbing it.

The following options are only available when using IMDversion 3:

• IMDsendPositions $<$ Send positions via IMD? $>$
  Acceptable Values: yes or no
  Default Value: yes
  Description: Specifies whether or not to send atom positions in angstroms via IMD.

• IMDsendEnergies $<$ Send energies via IMD? $>$
  Acceptable Values: yes or no
  Default Value: yes
  Description: Specifies whether or not to send energies (total, potential, Van der Waals et. al) in kilojoules/mol via IMD.

• IMDsendTime $<$ Send simulation time via IMD? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Specifies whether or not to send simulation time ( timestep in picoseconds, simulation time in picoseconds and step number) via IMD.

• IMDsendBoxDimensions $<$ Send box dimensions via IMD? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Specifies whether or not to send box dimensions (as a 3x3 matrix) via IMD.

• IMDsendVelocities $<$ Send velocities via IMD? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Specifies whether or not to send atom velocities in angstrom/picosecond via IMD.

• IMDsendForces $<$ Send forces via IMD? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Specifies whether or not to send atom forces kilojoules/(mol*angstrom) via IMD.

• IMDwrapPositions $<$ Wrap positions sent to IMD? $>$
  Acceptable Values: yes or no
  Default Value: yes
  Description: Specifies whether or not to wrap atom positions sent to the IMD client.