7.5 Trajectory analysis OpenGL

VEGA can analyze a trajectory file of a molecular dynamic simulation, displaying the results with a 2D/3D/4D graphical representation. To make it, as first step, you must open the starting molecule structure, by selecting the File -> Open item of the main menu. Furthermore, you must open the analysis dialog, by clicking on Calculate -> Analysis and on Open button to select the trajectory file. At the present time, only the CHARMM .dcd format is accepted, but in the next releases the support will be most extensive.

Trajectory
file
Tarjectory analysis Operations
Information
about the
simulation
Output file


Buttons
  

 

 
7
.5.1 Selection

Into the Selection tab, you can select a specific conformation, putting the frame number or pressing the First, the Last and the Lowest buttons (lowest means: the lowest energy conformation), or dragging the orizontal slider. Press Cancel to close the window and retain the selected conformation.

7.5.2 Calculation

Clicking on this tab, you can calculate some properties for each conformation stored in the trajectory. You can show the results in the GraphEd or tou can save these in an output file (Show Plot checkbox).

Calculation tab

Checking Ignore waters, you can exclude the water molecules from the calculations. The properties, that you can calculate, are: dipole moment, molecular lypophilicity (MLP)*, polar surface area (PSA), surface area, surface diameter, volume and volume diameter. For the surface properties, you can specify the probe radius (e.g. for the solvent accesible surface) and the dot density, and for the volume properties you can put only the dot density. Higher values of dot density, give more precise results, but require more CPU time.

7.5.3 Measure

With this tab, you can mesure some geometric properties like distance, angle, dihedral torsion and angle between two planes (plane angle).

Measure tab

From the listbox, you must choose the defined distance, angle, torsion, etc and thus press Ok. To define a new atom selection, press Edit and the geometry Selection Tool is showed.

7.5.4 Animation

This tab controls the molecule animation based on the trajectory file.

Animation tab

You can Start and Stop the animation, change the animation Speed, Skip Frames, activate the animation Loop, set the Start and the End of the animation. Press the Undo button to jump at the beginning or at the end of the trajectory.

 


* This property calculation is available only in the full version of VEGA package.