Sim Form

As described in the chapter on Interactive Molecular Dynamics, VMD has the capability to work with a molecular dynamics program running on another computer, in order to display the results of a simulation as they are calculated.

The Sim form allows you to control the behavior of a molecular dynamics simulations which has been previously connected to through use of the Remote form. This form contains controls to change parameters for the simulation and to affect how VMD displays the results of the simulation. The form 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 form, the host machine, if any, of the molecular dynamics simulation to which VMD is connected is displayed. 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. If you have the dubious misfortune of receiving coordinates faster than VMD can process them, or if you simply don't care to receive coordinates very often, setting this transfer period higher will improve the performance of both VMD and the simulation.

• 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 frames. When this is 0, then when VMD receives a new frame it replaces the last frame in the animation list with the new frame, instead of appending it. When it is set to some number N larger than 0, then every Nth frame received from the remote simulation will be appended to the animation list, instead of being used to replace the last frame.

To change a parameter, select the line with the relevant parameter, and in the text entry area that appears enter the new value and press <return>. After you enter a new value, a command will be sent to the remote simulation to change it, and there may be some delay between when the simulation gets the command, acts on it, and the results propagate back to VMD.

In the central portion of the form is shown a status message for the chosen connection. A large browser near the bottom of the Sim form displays the different energy values for the system being simulated (kinetic, electrostatic, etc.), as well as the current timestep and the temperature. It is automatically updated each time a new atomic coordinate set (timestep) is received and stored in the VMD animation loop.

At the bottom of the Sim form are two buttons:

• The Kill button, which when pressed will terminate the remote simulation which is currently selected in the connection chooser. This will not delete the molecule stored in VMD's internal lists, it will just stop the remote program from executing (and thus stop the transfer of new timesteps from that program to VMD). You must go to the Molecule form and delete the molecule from that list to completely remove the molecule from VMD memory.

• The Detach button, which when pressed will sever the connection between VMD and NAMD, but will NOT kill the NAMD process. Instead, the simulation will be left running.