How the Connection Works

 

  
Figure 10.1: Schematic view of remote simulation connections.

Figure 10.1 shows schematically how the components used by MDComm, NAMD, and VMD work together. There are two computers involved: the Graphics workstation (where VMD\ runs), and the Compute workstation (where NAMD runs). They may be completely separate computers, but it is certainly possible for both of these machines to be the same (particularly if you are working on a multiple-processor computer such as an SGI Onyx). To begin, just VMD and rappd need to be running. When you display the `Remote Connection Setup' menu in VMD, and enter a username and hostname and ask to connect to that computer, VMD uses MDComm routines to contact the rappd process running on the requested computer, and if it is present VMD gets back two lists of data:

1. The names of all MD programs which rappd knows how to start.
2. The ID's of all MD simulation jobs which have been previously started on that computer by rappd, and which are still running.

After contacting rappd and getting these lists, VMD displays them and lets you either resume a connection to an already-running job (by selecting an item from the second list), or lets you set up and start a new simulation (by selecting an MD application from the first list).

To start up a new simulation, you choose the name of the MD program, and press the button to get the parameters. VMD then requests rappd to send over the list of parameters required to start up the simulation, such as the name of the molecular coordinate file, the temperature, the timestep, etc. When these have all been entered, you press the Start Simulation button; VMD returns the completed parameter list to rappd, which starts the following events in motion:

1. rappd verifies that all the parameters are correct, and then starts up the namdd daemon. namdd is given the parameter set, and knows how to start NAMD running. namdd is used also to buffer data moving between NAMD and VMD.
2. namdd starts up NAMD.
3. On the Graphics end, the daemon namd_consumer is started, which does for VMD what namdd does for NAMD -- it buffers the data flowing between the applications. Note that VMD can maintain multiple connections, and can display and control several simulations at the same time. A separate namd_consumer/namdd pair is started for each connection.
4. After NAMD starts up and reads in its coordinates, it starts sending the coordinates back via namdd to VMD.
5. rappd keeps note of the fact that this instance of NAMD is running, but does little else. Later, if the connection between VMD and NAMD is dropped, rappd knows how to re-establish this link.