7.5 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,
the Accelrys archive, CHARMM/NAMD .dcd, Gromacs .xtc, PDB MultiModel and Quanta conformational search .csr
formats are accepted.
Trajectory file |
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Operations |
Information about the simulation |
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Output file
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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 horizontal slider. The Energy Graph button opens the Graph
editor with the potential energy trace. 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 you 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: dipolar
moment, molecular lypophilicity (MLP)*, molecular lypophilicity index
(ILM, water cluster required), lipole (Broto & Moreau), lipole (Ghoose
& Crippen), polar surface area (PSA), root mean square deviation
(RMSD), surface area, surface
diameter, volume and volume diameter. For the surface properties,
you can specify the probe radius (e.g. for the solvent accessible 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. Check Ignore
waters to ignore the water molecules in the calculation, Show plot to
show the results in the Graph editor and Consider selected atoms only to
calculate the property considering the visible atoms only.
7.5.3 Measure
With this tab, you can measure some geometric properties like distance, angle, dihedral torsion and angle between two planes (plane angle).
From the list box, 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.
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.