6.5 Trajectory analysis | ![]() |
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 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 |
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Operations |
Information about the simulation |
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Output file
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6.5.1 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.
6.5.2 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).
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.
6.5.3 Measure
With this tab, you can mesure some geometric properties like distance, angle, dihedral torsion and angle between two planes (plane angle).
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.
6.5.4 Animation
This tab controls the molecule animation based on the trajectory file.
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 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.