Bioactive Conformational Ensemble Help - Subsets Trajectories
Trajectories
The Trajectories tab shows important information about the Molecular Dynamics simulation computed. The section is divided in 4 sub-sections, which can be selected in the top-right corner of the window:View
The View section presents the set of parameters (METADATA) used in the biased molecular dynamics simulation, statistics of exchanges (when applicable) (REMD STATS), and an interactive 3D representation of the total number of snapshots computed, typically 10,000 (3D VIEW).
The metadata table contains the minimum information needed to reproduce the simulation: biased MD information (e.g. method, nº of replicas, length of the simulations, force field, solvent model) and system information (e.g. nº of atoms, simulated charge, box size, box type).
The REMD stats table presents the number of exchanges, average and associated probabilities for the replica exchanges occurred during the simulation. Complete exchanges paths for every replica can be followed in the extended plots available from the Open Replica Exchange chart button.
The 3D View NGL widget shows an interactive visualization of the lowest temperature/scaling factor (first replica) trajectory. Player buttons and a time slider give control to an easy visualization across all the trajectory frames.
The lowest temperature/scaling factor (first replica) trajectory represented in the 3D view is the one chosen for the whole set of BCE analyses, and can be easily downloaded from the top right Download PDB + Trajectory button. A PDB-formatted file will be generated and integrated in the download tar.gz file to be used as a topology.
NOTE: all the analyses computed and presented in the BCE analyses section (PCA, Cluster, Dihedrals, QM) have been computed on the lowest temperature/scaling factor (first replica) trajectory.
RMSd
The RMSd section presents the Root Mean Square deviation calculations done on the trajectory generated by the lowest temperature/scaling factor replica. A table at the top of the page shows average and standard deviation values for the whole trajectory in Ångstroms, whereas a chart plot at the bottom displays the variation of these values along time.
Two different methods were used to compute the RMSd, the classical Cartesian RMSd (RMSd), and the internal distance RMSd, where the distances computed are atomic internal distances, between every atom within the molecule (RMSdist). Besides, two different reference frames were used: the first snapshot of the trajectory (first) and the experimental structure (exp). The combination of these terms produced 4 different observables: RMSd_first, RMSd_exp, RMSdist_first and RMSdist_exp.
The default chart representation draws a reduced set of values (e.g. 100 points from a 10,000 snapshots trajectory). The complete chart containing all computed points is represented switching off the Reduced chart version (top right). Please note that with this representation, just one of the 4 different observables can be plot at the same time. To change between them, just click on the corresponding table row.
The chart presenting the results is interactive: it can be zoomed in/out and the values visualized can be shown/hidden clicking at the corresponding legend square boxes. A time slider is added to reduce the window time and can be then used to scroll the desired time-window left and right (see https://www.youtube.com/watch?v=oRjytvcWrWw for a real-time example). Placing the mouse pointer on the chart lines will automatically show the analysis values for the particular time point.
RGyr
The RGyr section presents the Radius of Gyration calculations done on the trajectory generated by the lowest temperature/scaling factor replica. A table at the top of the page shows average and standard deviation values for the whole trajectory in Ångstroms, whereas a chart plot at the bottom displays the variation of these values along time.
Four different values of RGyr are presented: the classical radius of gyration (Rgyr) and the radii of gyration about the x-, y- and z-axes, as a function of time (RgyrX, RgyrY, and RgyrZ).
The default chart representation draws a reduced set of values (e.g. 100 points from a 10,000 snapshots trajectory). The complete chart containing all computed points is represented switching off the Reduced chart version (top right). Please note that with this representation, just one of the 4 different observables can be plot at the same time. To change between them, just click on the corresponding table row.
The chart presenting the results is interactive: it can be zoomed in/out and the values visualized can be shown/hidden clicking at the corresponding legend square boxes. A time slider is added to reduce the window time and can be then used to scroll the desired time-window left and right (see https://www.youtube.com/watch?v=oRjytvcWrWw for a real-time example). Placing the mouse pointer on the chart lines will automatically show the analysis values for the particular time point.
Fluctuation
The Fluctuation section presents the atomistic fluctuations computed on the trajectory generated by the lowest temperature/scaling factor replica. A couple of tables at the top of the page show:
- Average and standard deviation values for the whole trajectory in Ångstroms.
- Fluctuation by each of the atoms within the molecule (in Ångstroms). A chart plot at the bottom is graphically displaying these values, whereas an NGL viewer at the right part is representing the 3D-structure, with a heatmap color gradient applied to the molecule atoms, from white (no fluctuation) to red (high fluctuation).
The three components presented are interconnected. Placing the mouse on top of a particular table row will highlight the corresponding atom in the bottom chart and also in the NGL viewer, and the same behavior will be obtained if placing the mouse on top of a particular atom of the 3D representation or the chart plot.
