Mol 或者 Molecules样式显示了加载分子的整体状态。VMD可以同时显示任意数量的分子。每个分子都可以单独隐藏起来，固定在适当的位置（例如，避免受到鼠标旋转命令的影响）。Form包含用于改变分子（单独或成组）状态的控件。

位于中心的browser显示有关每个分子的信息。The Name是包含拓扑信息的文件名，后跟一个唯一的整数ID，该ID在加载时由VMD分配给每个分子。原子显示分子中的原子数，框架显示与文件关联的时间步数，源显示文件或远程，反映信息是从文件获取还是从远程模拟获取。

每个分子旁边是一组状态标志，它们指示每个分子的当前状态。每个分子具有以下特征，可以打开或关闭:

• Top (T)
  Top indicates the default molecule used in the text commands when nothing is specified for the mol text command. It is also used in some forms (like Graphics and Animate) to determine certain values. There can be only one top molecule at a time.

  There is one unique molecule, called the top molecule top molecule, which is used to determine some parameters, such as the center of view, the data in the animation form, etc.
  

• Active (A)
  Several commands and actions in VMD operate on many molecules. These commands, unless specifically specified otherwise, will do their action for all the active molecules.

  VMD中的几个命令和动作可作用于许多分子。除非另有特别说明，否则这些命令将对所有active分子起作用。
  

• Drawn (D)
  If a molecule is Drawn then it is being displayed in the graphics display window. This is useful for temporarily hiding a molecule from view without deleting it.

  如果一个分子为drawn状态，则将其显示在图形显示窗口中。这对于暂时隐藏分子而不删除它很有用。
  

• Fixed (F)
  Fixed molecules do not undergo rotation, translation, or scaling. Note that while it may seem that one molecule has been moved relative to another, the difference is only apparent. The internal coordinates do not change when a standard rotation is applied by using, for example, the mouse. It is possible, however, to change the coordinates of atoms in a molecule, using the text command interface, and by using the atom move picking modes.

• Fixed  molecules不会旋转，平移或缩放。注意，虽然看起来一个分子相对于另一个分子已经移动了，但差异只是表面上的。使用鼠标进行标准旋转时，内部坐标不变。但是，可以使用文本命令界面和原子移动拾取模式来更改分子中原子的坐标。