8.6 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 button to select the trajectory file
or dragging a file over the trajectory analysis window and dropping it. At this time,
the Accelrys archive, AutoDock 4 DLG, BioDock 3.0, CHARMM/NAMD .dcd (little and big endian),
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).
Trajectory file |
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Operations |
Information about the simulation |
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Output file Buttons |
8.6.1 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. If Show frame is checked, the frame number and the total number of frames are shown in the workspace. Press Cancel to close the window and retain the selected conformation.
8.6.2 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 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 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 the property 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 switching 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: 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 Show plot
to show the results in the Graph editor.
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:
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).
8.6.3 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 Selection Tool is shown.
8.6.4 Cluster analysis
Thanks to this tab, it's possible to cluster the conformations of a trajectory file on the basis of the coordinates or torsions.
Three cluster methods are available:
Torsion, Torsion RMS and Coordinates. The first two methods
only allow to select torsions, clicking the Edit torsion button that
shows the selection tool. 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, the
RMSD field is enabled, but the meaning is much different for the two
methods: for the first one RMSD is the root mean square deviation in degrees
between the torsion values of two conformations, and for the second one it's the
root mean square deviation in Å between the 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:
CLUSTER_NUMBER | Number of the cluster starting from 1 to N, where N is the total number of clusters. |
ENERGY | Energy of the best conformer in the cluster (kcal/mol). |
CLUTERED_CONFORMATIONS | Number of conformation classified in the cluster. |
TORSTEP_1 TORSTEP_2 ... TORSTEP_N |
Torsion step defining the cluster. If the torsion steps are 6, and the step of the first torsion is 0, it means that the conformation in the cluster have the first torsion in the range form 0 to 60 degrees (e.g. 3 in the 180 to 240 range). These fields are available for the Torsion method only. |
Checking Active atom only, only the
active (visible) atoms are considered in the cluster analysis and checking
Sort by energy, the resulting cluster are sorted by energy (from the lowest
to the higher).
Clicking the Ok button the 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 the trajectorty doesn't have
the energy of each conformation. 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). The Quanta/CHARMM .csr file only contains the
energies of each conformation stored in it.
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.