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 Sim form, there is a chooser which lists the currently- and previously-active simulation connects. Each time a connection is made, a new item is added to this list. As most of the controls in this form only affect the connection selected in this chooser, select there the simulation you wish to control. The informative displays in the Sim form will only reflect the state of the chosen connection
Below the connection chooser is a browser used to set modifiable parameters in the simulation. It will display the current state of these parameters, and can be used to modify them. To make a change, 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 will be shown a status message for the chosen connection, and below this there is a chooser to turn on or off the display of patches for the simulation. The molecular dynamics program NAMD, which VMD is capable of communicating with, has the ability to run in parallel on several processors. It uses a spatial decomposition strategy to parallelize the task of computing the forces on each atom, where the volume of space occupied by the molecule is divided into uniform blocks, called patches. Each patch is assigned to a processor, and these patches may be moved between processors to balance the computational load. VMD can display a visual representation of these patches, and color the boxes according to different criteria. If you are using NAMD (or another program with similar parallel decomposition data that is being transmitted to VMD), you can turn on or off the display of these patches by using the chooser in the middle of the Sim form.
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:
As described for the Remote form, a molecule loaded via a remote connection acts just like any other molecule, with the extra abilities/options available via the Sim form. Once the connection is shut down, you can still use the Animate form to play the stored frames back (this can even be done while the simulation is active and connected).