8.5 Trajectory analysis

VEGA ZZ 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, the Accelrys archive, BioDock 3.0, CHARMM/NAMD .dcd (little and big endian), ESCHER NG, Gromacs .xtc, IFF/RIFF, MDL Mol multi-model, Tripos Mol2 multi-model, PDB multi-model and Quanta conformational search .csr formats are accepted and the file size limit is 16 Exabytes (17.179.869.184 Gb, for more information see the FAQ section).


Trajectory
file
Tarjectory analysis Operations
Information
about the
simulation
Output file


Buttons
  

 

 
8
.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.

8.5.2 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).

Calculation tab

Checking Ignore waters, you can exclude the water molecules from the calculations. The properties, that you can calculate, are: dipolar moment, gyration radius, 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.
The Advanced button is enabled when you select the RMSD calculation. Clicking on it, a file window is open in witch is possible to change the advanced options for the RMSD type:

RMSD advanced options

In this window, it's possible to select the reference structure (set of coordinates) used in the RMSD calculation. It can be a specific frame in the trajectory (default 1), the previous frame and a specific molecule file. Please remember that this file must be compatible with the molecule used for the molecular dynamics calculation and in other words it must be the same molecule. The Previous frame RMSD type is useful to measure the RMSD between subsequent frames and implicitly the velocity of the molecule movements (remember that the time step is constant during the simulation). 

8.5.3 Measure

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

Measure tab

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 shown.

8.5.4 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.