IMD Connect Simulation Window

VMD has the ability to work with a molecular dynamics program running on another computer, to interact with and display the results of a simulation as they are calculated. A major feature in VMD is the ability to add perturbative steering forces to a running simulation, which are incorporated directly into the dynamics calculation; we refer to this capability as Interactive Molecular Dynamics (IMD). In order to run and IMD simulation it is necessary to have a molecular dynamics program that supports the IMD communication protocol. To date, two such programs exist; NAMD, developed at University of Illinois, and Protomol, developed at Notre Dame. The rest of the discussion in this chapter assumes you are using NAMD. See the NAMD home page for information on obtaining NAMD.

Interactive Molecular Dynamics

IMD works by establishing a TCP connection between VMD and the molecular dynamics simulation program. NAMD, or whichever MD program is being used, acts as the server. In order to prepare NAMDto accept VMD's IMD connection request, NAMDmust be configured to listen for incoming connections on a network port. Once NAMD has started up, may wait for the user to connect through that port. When VMDconnects to NAMDsuccesfully, the simulation commences. Before connecting to the remote simulation, the VMDuser must first load a molecule corresponding to the system being simulated. The structure file should correspond to the same structure file used by NAMD. Once the molecule is loaded and NAMD has been started and is listening for a connection, you are ready to connect to the simulation and start receiving coordinates. To establish a connection, open the Simulation window, enter the hostname on which NAMD is running and the port on which NAMD is listening for incoming connections, then press the Connect button to establish the connection. If NAMD is running on several distributed nodes, VMD must connect to the root node on which NAMD initially started out.

IMD Using the Simulation window

The Simulation window allows you to control the behavior of a molecular dynamics simulations which has been previously connected to through use of the Remote window. This window contains controls to change parameters for the simulation and to affect how VMD displays the results of the simulation. The window also contains informative displays, which show the current status of the simulation connection, and such things as the current energy, temperature, and timestep of the molecular system being simulated.

At the top of the window are two entry fields and a button for establishing a connection to a running MD simulation. Enter both the hostname on which the simulation is running, and the port on which the simulation is listening, then press the Connect button to establish the connection. See the text console for possible error messages and status updates. Below the connection display is a browser used to set some connection parameters. These include:

• Transfer Rate: How often a timestep is transferred from the remote simulation program to VMD. By default, this is 1, which means every calculated timestep is sent. If this is set to some value N, then only every Nth step will send from the remote computer, thereby decreasing the amount of network processing and rendering that needs to be done.

• Keep Rate: How often VMD saves the timestep in its animation list, instead of just discarding it after displaying it. By default, this is 0, which means that VMD does not save any timesteps. When this is 0, then when VMD receives a new timestep it replaces the last timestep in the animation list with the new timestep, instead of appending it. When it is set to some number N larger than 0, then every Nth timestep received from the remote simulation will be appended to the molecule.

Parameters may be changed by entering text into the appropriate entry field and pressing <return>. When a new value is entered, a command is sent to the remote simulation to change it. There may be some delay between when the simulation gets commands, acts on them, and the results propagate back to VMD. Connection state is shown in the center of the window. The simulation status text area displays energy values for the system being simulated (kinetic, electrostatic, etc.), as well as the current timestep and the temperature. It is updated each time a new coordinate set (timestep) is received by VMD. The Stop Sim button will terminate the remote simulation, but will not delete the molecule in VMD. The Detach Sim button will sever the connection between VMD and NAMD, but will allow the simulation to continue running.