8.6 Trajectory analysis

VEGA ZZ can analyze trajectory files of MD simulations, displaying the results by a 2D/3D/4D graphical representation. To analyze a MD trajectory, as first step, you must open the starting molecule structure, 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 or dragging the file over the trajectory analysis window and dropping it. At this time, the Accelrys archive, AutoDock 4 DLG, AutoDock Vina PDBQT multi-model, BioDock 3.0, CHARMM/NAMD .dcd (little and big endian), CIF multi-model, ESCHER NG, Gromacs TRR. 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).

You can open a trajectory file in several ways:

1. As a normal molecule by clicking File Open menu item, double clicking in Explorer and performing drag & drop, but it's possible only if the trajectory format includes the molecule data (e.g. ARC, CIF, IFF, PDB, MDL and Mol2) or the correspondent molecule file is in the same path and has the same name of the trajectory (e.g. AutoDock DLG, BioDock, CSR, DCD, GRAMM, ESCHER, Mol2 multimodel, PDB multimodel, TRR and XTC).
2. You can open the molecule file and thus in a second time the trajectory file by the trajectory analysis window. This second method allows you to open trajectories with a name (prefix) different from that of the molecule file.
3. You can open other molecular objects but only AFTER that you opened the trajectory.

Trajectory file		Operations
Information about the simulation
		Output file Buttons

 
8.6.1 Selection

In Selection tab, you can select a specific conformation, putting the frame number or pressing First, Last and Lowest buttons (lowest means: the lowest energy conformation), or dragging the horizontal slider. The Energy Graph button opens the Graph editor showing the potential energy trace. If Show frame is checked, the frame number and the total number of frames are shown in the workspace.

8.6.2 Calculation

Selecting this tab, you can calculate some properties for each conformation stored in the trajectory. You can show the results in the Graph editor or you can save them to an output file (Show Plot checkbox).

Checking Exclude invisible atoms, you can exclude the unselected (invisible) atoms from the calculations. The invisible atoms are totally ignored and the visible atoms are considered as a whole molecule. This option is useful when you want to calculate the solute area in a solvent cluster: unselecting the solvent, its contribute in the surface calculation is totally ignored.
Checking Consider selected atoms only, you can calculate properties considering the visible atoms only. In the case of the surface area, the unselected (invisible) atoms are considered to compute the overlap of the Van der Waals spheres, but not in the area evaluation. In other words, the area obtained enabling this option is lower than the Exclude invisible atoms because the contribution of the overlapped zones is subtracted. The Consider selected atoms only is useful when you want calculate the surface of a protein domain or a substructure in a generic molecule.
The calculable properties are: dipole moment, gyration radius, molecular lypophilicity (MLP), molecular lypophilicity index (ILM, water cluster required), lipole (Broto & Moreau), lipole (Ghoose & Crippen), ovality, polar surface area (PSA), root mean square deviation (RMSD, RMSD with H, RMSD alignment, RMSD alignment with H, RMSD with symmetry correction and RMSD with symmetry correction with hydrogens), surface area, surface diameter, volume and volume diameter (for more information, click here). For the surface properties, you can specify the probe radius (e.g. for the solvent accessible surface) and the dot density; 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 Show plot to show the results in Graph editor.
The Advanced button is enabled when you select the RMSD calculation. Clicking it, a dialog window is shown in which it's possible to change the RMSD options:

In this window, you can select the reference structure (set of coordinates) used in RMSD calculations. It can be a specific trajectory frame (default 1), the previous frame and a molecule file. Please remember that this file must be compatible with the molecule used for the molecular dynamics simulation and, in other words, it must be the same molecule. 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).

8.6.3 Measure

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

In the list box, you must choose the geometric property that must defined by Selection Tool clicking Edit. To perform the calculation, you must press Ok button.

8.6.4 Cluster analysis

Selecting Cluster tab, it's possible to perform the cluster analysis of the conformations on the basis of coordinates or torsions.

Three cluster methods are available: Torsion, Torsion RMS and Coordinates. The first two methods require to select torsions by Selection Tool, clicking the Edit torsion button. The torsions are listed by name (Torsion column) and torsion steps (Steps column) and they can be included or excluded checking or unchecking them. The context menu allow to un/check all torsions (Check all, Uncheck all), to un/check all selected torsions (Check selected, Uncheck selected) and to un/select all torsions (Select all, Unselect all). If the clustering method is Torsion, it's possible to change the steps in which the 360° angle is subdivided (e.g. 6 means clusters of 0, 60, 120, 180, 240, 300 degrees for each torsion angle), selecting one or more torsions in the list and changing the value in the Steps field.
If the clustering method is Torsion RMSD or Coordinates, RMSD field is enabled, but the meaning is much different: for the former, RMSD is the root mean square deviation in degrees between torsion values of two conformations, and for the latter, it's the root mean square deviation in Å between atom coordinates of two conformations.
Checking Save energy, a .ene file in CSV format is saved using the clustered trajectory as base name. The format of the CSV file is:

CLUSTER_NUMBER; ENERGY; CLUTERED_CONFORMATIONS; TORSTEP_1; TORSTEP_2; TORSETP_N

where:

Checking Active atom only, the active (visible) atoms only are considered in the cluster analysis and checking Sort by energy, the resulting clusters are sorted by energy (from the lowest to the higher).
Clicking Ok, Save trajectory file requester is shown in which it's possible to change the name and the format of the clustered trajectory.

WARNING:
It's impossible to perform the cluster analysis if each conformation has a unknown energy. It means that you must have a file containing the energies (e.g. the .ene file generated by the AMMP conformational search, the NAMD output file, etc). Quanta/CHARMM .csr format is the only one that contains the energies of each conformation.
If the energies are inaccessible, the Ok button is disabled. 

8.6.5 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.