VMD uses several different GUI forms, each designed to control a specific aspect of the molecular display (e.g., to control the appearance of the graphics display window, or to change the colors of displayed objects). Each form has a unique name, includes a button with the name of the form near the top of the window. Pressing this button will hide the form from view. The following sections give a brief description of the forms available in VMD ; the remaining chapters in this manual describe the actions which these forms make available in greater detail.
The Main form, also called the button bar, can turn most of the other forms on or off (including two ways to turn itself off!). It can also be used to start an HTML viewer to see the general help file, and to exit the program. The buttons with lights control which forms are turned on or off; if the light is on, the form is being displayed. Sometimes a form is turned on but is hidden behind other forms or windows. A quick way to bring the form to the top is to turn it off then on again.
The button bar can be closed by clicking on the Main button and, as with all other forms, by clicking on the button in the center top. There are several ways to re-open the form. The simplest is to go to the window labeled GL Display and use the pop-up menu that appears when you press the right mouse button described here to select `Show Form' followed by `main'. It can also be turned on with the text command menu main on.
The Help button starts up an HTML viewer (such as Mosaic or Netscape) to view the help file (see General Help).
Press the Quit button to exit VMD . This will bring up another form which verifies that you do indeed wish to exit. Press Yes to quit, or No to return to VMD .
The Mol, or Molecules, form shows the global status of the loaded molecules. Any number of molecules may be displayed by VMD simultaneously. Each molecule can separately be hidden from view, fixed in place (e.g., prevented from being affected by mouse rotation commands). This form contains controls to change the status of the molecules individually or in groups.
The Load From Files button will activate the Files form (section 3.3.3), which is used to read a new molecular structure in from a file or set of files. Similarly, the Setup Remote Connection will display the Remote form (section 3.3.12) which is used to initialize or connect to a simulation running on a remote computer. Chapter 4 describes fully how to load a molecule and what file formats are supported.
The browser at the center displays information about each molecule. The Name is the file name which contained the topology information, followed by a unique integer ID which is assigned to each molecule by VMD when it is loaded. Atoms shows the number of atoms in the molecule, Frames gives the number of timesteps associated with the file, and Source is either File or Remote, reflecting whether the information was acquired from a file or a remote simulation.
Next to each molecule is a set of status flags, which indicate the current Status of each molecule. Each molecule has the following characteristics, which can be on or off:
The status of a given molecule can be changed by selecting the molecule in the browser and pressing the toggle that controls the appropriate flag. The active, drawn, and fixed status values can be changed for several molecules at one time by selecting several molecules before pressing the toggle. However, only one molecule can be top at any one time, so Make Top can only be applied to one selection. Pressing one of the All ... or No ... buttons either sets or unsets corresponding flag on all the loaded molecules.
The Single A/D/T button makes the selected molecule active, displayed, and top. It also resets the scene so the given molecule roughly fills the screen. It is a quick way to switch from viewing one molecule to another when it is desirable to only show one molecule within the graphics display window at a time.
The Delete button deletes all selected molecules. There is no prompt verifing the deletion, so take some care. If a deleted molecule was the top molecule, a new top molecule will be set from the remaining structures.
The Files form is used to load a file from disk. It is not accessible via the button bar on the Main form. Instead, use the Load From Files button in the Molecules form or select the `files` submenu in the `Show Form' option available from the popup menu in the graphics display.
To use this form, first select the appropriate file type from the browser on the left (the available file types are described here). One or two text input lines (depending on the molecular structure and coordinate file formats selected) will be displayed in the center of the screen. These need to be filled with the appropriate file names, which can be done in two ways. The easiest is to press the button to the left of the text area to bring up the file browser. The other way is to type the name directly into the text area.
Once you've selected the correct file (or files), press the large button that says Load Molecule. The button will disappear and be replaced with a message that says Loading ... Please Wait. After the files are completely processed, the structural information will be displayed in the text window, and the Files form will be closed automatically.
The Graphics form is the most complicated form in VMD , which could be expected from a visualization program. The details of most of the subjects discussed below are covered in the special topics on selections, drawing methods, and coloring methods. In short, a molecule can have many different representation, also referred to as views. Each view consists of three parts: a selection, a drawing method, and a coloring method. The selection determines which part of the molecule is drawn, the drawing method defines which rendering representation is used, and the coloring method gives the the color of each part of the representation.
There are actually two parts to the graphics form. The Image Controls button brings up the controls used to alter the drawing and coloring methods. The Atom Name Lists button provides access to browsers which display the lists of atom names, residue names, and so forth for the selected molecule.
This form is used to control the appearance of one molecule at a time. The molecule is affects is selected in the `Selected Molecule' chooser at the top of the form. The browser below this chooser lists the views available for the molecule. Each line of the browser shows information about the drawing style, the coloring method, and the selection which completely specify the view. To change the attributes of a given view, click on the view that should be changed. The atom selection for that view will appear in the Atom Selection text area and, if the Image Controls button is pressed, the drawing and coloring method choosers will also change to reflect the current view.
To add a new view of the molecule, enter the selection into the Atom Selection text area (or keep what is there) and press Create New. This adds the view to the currently selected molecule. The Add to Active button can be used to add a new view with the same selection to all the active molecules. (This feature is not used very often and may be removed in future versions.)
To delete a view, select the view in the browser and press the Delete button. Bear in mind that this does not delete the molecule, it only deletes a view of the molecule. (To delete the molecule, use the Mol form .)
The drawing method indicates how the view's selected atoms are displayed in the graphics display window, and the coloring method indicates how to color the displayed atoms. The selected view's drawing and coloring methods are changed via the corresponding chooser. Some of the methods have additional controls which will appear when that particular method (either drawing or coloring) is chosen. The controls for the drawing method are:
When the Atom Name Lists button is pressed, two browsers appear in place of the drawing and coloring method controls. These are used to list the available keywords and values for use in choosing atoms for the selected views. The left browser contains a list of the keywords and functions understood by the selection command. If a keyword is selected which can take on a value (for instance, name and index), then the possible names will be displayed in the rightmost browser. The functions can be identified by the ( to the right of the name. After selecting a keyword, the right browser will display all the names associated with the keyword. For example, selecting resname in the left browser will show all the three-letter residue names known for the selected molecule.
Clicking on a field in the value browser will add it to the selection text field. Double clicking a keyword field adds the keyword to the text field. A double click is used so that the single click is available for simple viewing of the possible keyword values.
In addition to adding or removing views from a molecule, this form is also used to change how an existing view is displayed. After selecting a view for a specific molecule, the form's controls are updated to show the current settings for that view. Changing the settings will automatically change the respective view, and the new format will be shown in the graphics display window. The display will be updated after every change, however, which is sometimes not always desireable (for example, if a number of different aspects need to be changed at once). The Apply Changes Automatically button may be toggled off to change this behavior -- if it is turned off, selected changes will only be applied when the Apply Changes button is pressed. Selecting a different view, or pressing the Clear Changes button, before applying the changes will reset the form controls to the current settings of the selected view.
To clear the selection text for a given view double click on the Clear Changes button. The first (and every odd) click reverts the text to its previous setting, the second (and every even) click clears it completely.
Each molecule displayed by VMD can contain multiple sets of atomic coordinates, which may be played back to animate the molecule and show its motion. The source of the coordinates can be, for example, from a molecular dynamics simulation, or simply multiple versions of the same molecular structure. The Animate form is one way to control the playback of these trajectories.
The Animate form handles the trajectory playback of the active molecules. The second line of controls contains five buttons which act like the buttons on a tape player or VCR. The center button (with the square) stops the animation. The button to the right of the stop button advances the animation one step forward in the trajectory, and the next button to the right continually steps the animation forward. Similarly, the buttons to the left of the stop button steps the animation backwards either once or continuously. (Just remember that the button that looks like fast-forward is really the play button, and that the one that looks like the play button is really the single step forward button.)
The molecular status shown in this form reflects the state of the top molecule. Commands entered via this form, however, affect all active, not just the top molecule. This makes it possible to position several different molecules at the same frame, and to start them in motion at the same time with one command. But, since it is not immediately obvious from the information shown in this form what molecules will be affected, some care must be taken to make sure you have the proper molecules active that you wish to animate.
The rate of playback can be controlled in two ways. The Frame Skip controls change the step size. By default, the frame skip is 1, so each step of the playback increases (or decreases) the animation by one frame. If the frame skip is 5 then the animation proceeds five times faster because only 1/5 of the frames are shown.
The Speed slider at the bottom of the form also affects the playback speed. Internally, this controls how many screen updates are needed between each step. By default, the slider is at the far right indicating that one step is performed for each screen redraw. Moving the slider to the left increases the minimum time required between updates.
The Start and End buttons are used to simplify the comparison between the initial and final structures - Start resets the current animation to the first frame, and End jumps to the last frame. If you need to jump to a specific frame, enter the frame number in the Jump To text area and press enter. One thing to bear in mind is that the frame number starts at 0, so to jump to the 5th frame, you must actually enter 4 here.
All of the controls affect the active molecules, but two parts of the animate menu use information from the top molecule. There is a display just below the End button which shows something like 0/1 or 23/59. The first number specifies the current frame number, starting at 0, and the second gives the total number of frames.
When the animation is playing forward and reaches the end of the data available for the top molecule, one of three possible actions takes place, as specified in the Style chooser. The default is `Loop', which will reset the active molecules to the first frame and continue playing forward. `Once' will stop the animation when it reaches the last frame, and `Rock' reverses the direction of animation. The actions are symmetrical when the animation is playing in reverse.
This form is used to add, save, or delete coordinates sets (also referred to here as frames) from a molecule. Usually these coordinates come from successive frames of a trajectory but, as shown in the tutorial A Quick Animation, can also be distinct conformations of the same structure.
When this form is used, it will affect only the molecule selected in the Selected Molecule chooser. There are three types of actions which can take place; read frames from or write frames to a file (in either a DCD or PDB format) or delete frames from the current animation.
VMD can read in new coordinate sets from either PDB files (to add a single new frame to the animation), or from binary DCD files (which may contain frames). The new coordinate sets are appended to the end of the stored animation list for the selected molecule. At present, there is no way to use Babel to read non-PDB and non-DCD files. The format is determined by selecting the appropriate name in the File Type chooser. If you want to read in all the information from the file, make sure that the Amount chooser says `All', then press the Read button in the bottom right corner. This will bring up the file browser so you can select the file. (Unlike the Files form, the file is loaded immediately after the filename is entered in the file browser.)
Sometimes you may not want to read in a whole DCD file. For example, you may only want the last frame, or every tenth frame. You can do this by choosing the `Selected' option in the Amount chooser. This brings up the frame skip selection controls. Once you've chosen the appropriate values, press the Read button to bring up the file browser and finish as mentioned in the previous paragraph. The Amount options are ignored when reading in PDB files.
You can write the loaded frames to either a PDB or a binary DCD file with the `Write File' action. This may be used to write out a new trajectory in a single file after assembling many frames from different sources (such as PDB or DCD files, or even from a remote simulation). You can also use this, in combination with Read File, as a way to make PDB files from a DCD trajectory.
You can either save the entire stored trajectory, or a slice of the data by using the Amount chooser. Then select the appropriate output file type in the File Type chooser, and press the Write button in the bottom right corner. This brings up the file browser, which you can use to enter the new filename. Once you press the Write button in the browser, the file will be written without further confirmation.
This provides a way to delete frames from memory. First, choose the frames you wish to delete with the Amount chooser and (possibly) the frame skip controls, then press the Delete button. There is no confirmation of deletions.
One problem with this mechanism is there is no way to delete every frame except for those given by the frame skip. You can get around this by writing the skip selection to a DCD file, deleting all the frames from memory, then reading the skip back in from disk.
The meaning of this option varies depending on the action. If `All' is selected, then all the frames will be read from the file, or all the frames will be written to the file, or all the frames will be deleted from memory.
The other option is `Selected.' This will bring up three controls, labeled Begin, End, and Skip. These make it possible to use a subset of the frames, starting at frame Begin and selecting every Skip frames until the End is reached. For instance, to select every fifth frame between frames 14 and 98, set:
(Remember that frame numbers in VMD start at 0, so frame 0 is the first frame.) The value `-1' is a special number; setting Begin to -1 is the same as starting at the first frame, End = -1 is the same as ending at the last frame, and Skip = -1 is the same as taking one step.
When the Action is `Read File', the selection is applied to the frames from file to be read. When `File', the selection determines the frames to be written, and when `Delete Frames', the selection determines the frames to be deleted from memory.
This form is used to manipulate the labels which may be placed on atoms, and the geometry monitors which may be placed between atoms. Labels are selected with the mouse. Once selected, the Labels form can be used to turn different labels on or off or to delete them entirely. Also, labels displaying geometrical data such as bond lengths may be graphically displayed using this form.
The Category chooser (in the upper left) is used to select which category of labels to manipulate. The different label categories include:
followed by either the phrase (on) or (off). The last word indicates if the label is turned on or off.
A label can be turned on or off without deleting it, by selecting the label in the central browser and pressing the Hide button. To turn it back on, select it again then press the Show button. Press the Delete button to delete it. This browser allows multiple selections, which, for example, allows you to delete several labels at once. To select everything in the current category, press Select All; to unselect them, press Unselect All. If nothing is selected, the action is applied to everything. Thus, one way to turn everything off is to press Unselect All then press Hide. (It may seem counterintuitive, but it was done this way so all the labels could be deleted by just pressing Delete.)
If the label has a numeric value (such as a bond length geometry monitor), it is easy to graph the change of the value over time. The Graph button creates a temporary file for use by a graphing program, then optionally starts such a program to display the data. Each line of the file contains the frame number (starting at zero and expressed as a floating point number) followed by the value of the label for that frame.
Once the file is created, the text in Graph Command is executed to plot the data. By default, the text is xgraph %s, where the %s is automatically replaced with the appropriate temporary file name. When the graphing program finishes, the temporary file is deleted.
The default setup causes VMD to freeze until the graphing program finishes. It is possible to get around this by including an & at the end of the graph command, as in:
xgraph %s &This may sometimes cause a problem because VMD might delete the file before the program finishes reading it. If this is a problem, try:
csh -c "xgraph %s &; sleep 4"to cause VMD to wait a few seconds before deleting the file. You may have to increase the delay depending on the file size and type of program used. You may also try variations on the theme; for instance
csh -c "xterm -e vi %s ; sleep 4"will bring up a vi window with the data file.
The Display form controls many of the characteristics of the graphics display window. The characteristics which may be modified include:
The position of the clipping planes are changed with the Near Clip and Far Clip controls. It is not possible for the near clip to be farther away than the far clip. When using stereo, the near clip should be decreased, or even set to zero.
The screen height, along with the screen distance, defines the geometry and position of the display screen relative to the viewer. The screen height is the vertical size of the display screen, in `world' coordinates. Each molecule is initially scaled and translated to fit within a 2 x 2 x 2 box centered at the origin; so the screen height helps determine how large the molecule appears initially to the viewer. This parameter is used mainly to configure the VMD display to the dimensions and position of a large-screen display, such as a projector, that may be used as a stereo display.
Figure 3.17 describes the relationship between the screen height, the screen distance, and the world coordinate space.
VMD maintains a database of the colors used for the molecules and the other graphical objects in the display window. The database consists of several color categories; each color category contains a list of names, and each name is assigned a color. The assignment of colors to names can be changed with this form. There are 16 colors, as well as black (the VMD color map), and this form can also be used to modify the definitions of these 17 colors. For more about colors, see the section on Coloring.
To see the names associated with a color category, click on the category in the Category browser located on the left side of the form. Click on the name to see the color to which it is mapped. To change the mapping, click on a new color in the browser to the right of the Category browser. For instance, to change the background to white, pick `Display' in the left browser and `Background' in the center one. The right browser will indicate the current color (which is initially black for the background). Scroll through the right browser and select white to change the background.
Sometimes you may want to change the RGB value of a color in the color map, instead of changing which color is assigned to a particular name. For example, you may need to make a black and white picture and need to emphasize the contrast between a red oxygen and a yellow sulpher. This is done with the Edit Colors part of the form. First, choose the color you want changed in the browser. Then move the red, green, and blue sliders until you get the desired color. There are a few additional buttons to help you do this. The white button makes the color white (red = blue = green = 1.0) and the black color makes it black (red = blue = green = 0.0). The default button restores the color to its original RGB values. The tie button is used to make grey colors; when the button is depressed, as you move one slider the rest will follow. Press the tie button again to untie the sliders.
Several of the coloring methods in the graphics form are used to color a range of values, as compared to a list of names. The actual coloring is determined by the color scale.
There is only one color scale available at any one time (out of the three possible) and it is changed with the Color Scale Method chooser. Changing the values of Minimum and Midpoint change some the proportionality values used in making the scale.
The colors used by the color scale are not the colors in the color map, so the Edit Colors part of the form will not affect the color scale colors.
This form is used to create a file with an image of the currently displayed graphics scene. VMD can write input script files for a number of image processing packages. These packages are listed in table 8.1. Once VMD creates an input script in one of the supported formats, the particular package can use this file to create a final output image. See section for more information on how rendering is performed.
The rendering process works in two stages. The first step writes an input file for the image processing program selected in the Output Formats browser, and the second (optionally) starts the rendering process. The file is given the name entered in the Output Filename field; a default name is given when a new format is selected, so it is best to hold off entering the filename until after the file format is selected. Another way to select the filename is available by pressing the List... button, which opens up a file browser.
Pressing the Go button writes the data file. After that, the Render Command is executed. The default command should start the appropriate rendering program if it is available.
The fastest of the currently supported programs is Raster3D. The rendering command for it has been set up to call the SGI program ipaste when the RGB output file is finished. VMD will wait for the rendering to finish, which causes VMD to freeze, so you may want to run the job in the background. This can be done by enclosing the existing text with ()'s and putting an & at the end. For example, the way to make the Raster3D render command run in the background is:
(render < %s -sgi %s.rgb; ipaste %s.rgb)&
There are some issues to consider when using the rendering commands, which can lead to discrepancies between the scene displayed in the VMD graphics display window and the image generated by the image processing application. These issues include:
The following description assumes you have read the section on the 3D user interface and understand how the UNC trackers work in your installation. Since few outside this research group will have the required tracker hardware and the library, we will not describe this capability in any great detail. We suggest that if you want more information, please contact us via email to vmd@ks.uiuc.edu .
The Tracker form is used to control external 3D pointers and tools. This form is actually two forms, one for Trackers and the other for Tools, as selected by the appropriately labeled buttons on the second line.
A Tracker is an external device capable of measuring the spatial (3D) position of one or more Sensors. The Available Trackers browser allows you to start a tracker with a given number of sensors. Most of the selections are for various UNC trackers, but only the Fastrak has been tested in the last two years. (The CAVE tracker is started automatically when the CAVE display is used.) The text emulation modes do not start a physical tracker but instead start a `software' tracker with position and orientation values which are never updated. The tracker command can then be used to overrride the current tracker coordinates and move the tool by hand. Indeed, that is how an external gesture user interface component has been tested with the program.
Press the Start Running button to start the tracker selected in the available browser. Be warned that there is a limitation in our interface to the UNC tracker library which does not allow you to try to start the same tracker more than once. Usually this isn't a problem, but sometimes the tracker doesn't work the first time (this usually happens when VMD previously exited accidentally while connected to the tracker. If the tracker doesn't start but you need to use it, the only thing to do in this case is quit VMD and try again.
The running trackers are listed in the lower browser. Only two things can be done to a tracker if selected: pause or unpause. When paused, none of the sensor coordinates will be updated. There is currently no way to delete a running tracker.
A Tool in VMD is a sensor configured to perform a particular task. The user can move the sensor about in space, and the tool connected to that sensor can then be used to perform an action. There are two types of tools: pointer (the default) or grabber. Each sensor can be configured as a different kind of tool. To make the first pointer into a grabber, select the tool in the browser and choose `grabber' in the chooser. When you want to return to the pointer, choose `previous'. The Length, Scale, Detail, and Offset controls modify the corresponding values in the currently selected tool. Modifying these values changes how the tool is represented graphically, and where it is positioned in space.
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 Remote form, along with the Sim form, are used to start up and connect to a molecular dynamics simulation on a remote computer, and to control the state and visual display characteristics of that simulation. VMD can display any number of different connections simultaneously. The Remote form is used to establish a connection, while the Sim form is used to control a connected simulation. To do all this, VMD uses the MDComm daemons and library, which have been developed by Rick Kufrin at the National Center for Supercomputing Applications. Before using the information in this section, however, you should first read the chapter on Interactive Molecular Dynamics, which describes how this capability is installed and how it functions.
The Remote form has the following uses:
The first step in starting a new simulation, or in attaching to a running simulation, is to establish a connection with the MDComm control daemon (called rappd) on the remote computer. Enter the machine name and username in the given text areas, and press the Connect button. This then directs VMD to connect to the remote MDComm daemon, which will return information about available applications, and running jobs, on that computer.
After the connection is established, two browsers will be shown:
After an application to start has been selected, and the parameters have been returned by pressing Get Parameters, a large browser will fill the form which is used to change the values for all the necessary simulation program parameters. At present, only the program NAMD is available to be used in this capacity, so this following discussion will assume this is the program you are using.
Each line of the browser lists a variable name, a short description, a flag indicating if the value is required or optional, and an indicator telling if the input parameter is a string, integer, or float. Additionally, the required options and are shown in one color (hopefully in red, but your result may vary) while the optional ones are in another (like black). To change a line, select it and enter the new value in the text region which appears on the bottom of the form. Press Cancel to deselect the item without changing it.
When the simulation parameters browser is open but no items are selected, several options are available on the bottom of the form. Read from file allows you to set the options from a file while Write to file writes the file given the current parameter settings. Pressing Cancel returns the form to the mode which allows you to enter a new remote simulation host and a new user name.
Once all the parameters have been defined, run the simulation by pressing the Run Simulation button. You will need to go to the text window and enter the password for the remote account. This starts NAMD on the remote machine. If there are no problems, the new system will appear on the screen and be updated as each frame is computed.
After you have set up the parameters and pressed the Run Simulation button, or instead if you have chosen to attach to a running simulation, the structure and coordinates of the molecule being simulated will be transferred to VMD , and then VMD will continually update the molecule with new coordinates as soon as they are calculated by the remote computer. At this point, the Sim form is used to control the state of the remote simulation, to kill or detach the job, and to control how some aspects of the simulation are displayed by VMD . Even if other simulations are connected to VMD , you can use the Remote form after this to set up and start other connections.
When a connection is made, the molecular structure read from the remote simulation is added to VMD 's list of loaded molecules just as if it had been read from a file. As new coordinate timesteps are calculated by the simulation and sent to VMD , they are added to the internal animation list of that molecule, and can be played back using the Animation form and controls just as a `normal' molecule. In fact, you can read in new coordinate frames from PDB and DCD files and append them to the animation list of an on-line molecule just as with any other molecule. The main difference is that a molecule retrieved from a connected remote simulation will continue to get new data from that connection, until the connection is terminated. Such a molecule also has a few more options available for it, which are accessed through the Sim form (described next).
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).
There are some common parameters that may be modifed while a simulation is running. They are changed using the browser at the top of the Sim form just below the connection chooser. These include: