Trajectory Analysis

Analysis > Trajectory Analysis... gathers in a single window the analyses that read the frames of an object (molecular dynamics, scans, NEB, umbrella sampling, imported trajectories). The analyses are grouped in a list on the left; the options of the selected analysis appear below it, and the results are shown on the right as a plot (with several Views for some analyses), a Table and a Summary (Figure 1).

Input (top of the window)

• System / Object: the trajectory.

• First frame / Last / Step: the frames analyzed (Last = -1 means the last frame).

• Time per frame (ps): the time between frames; 0 plots against the frame number.

• Atom set: the Whole object or the Current selection in the 3D view. Ignore water and ions leaves water and single-atom ions out of the atom set.

Click Run; long analyses run in the background and can be cancelled. Export Image... saves the plot and Save Data... the numbers.

Available analyses

Structure

• Radius of gyration: Rg of the atom set in every frame (optionally mass weighted).

• Secondary structure (DSSP): DSSP (Kabsch and Sander, 1983) for the protein residues of the atom set, shown as a residue × frame map (Figure 1) and as the fraction of each structure type per residue. Missing amide hydrogens are placed by the DSSP rule. Clicking the map goes to that frame.

• Solvent accessible surface (SASA): Shrake–Rupley SASA of the atom set alone (probe radius, default 1.4 Å; points per atom, default 100).

Interactions

• Hydrogen bonds: GROMACS criterion (donor–acceptor distance, default 3.5 Å; H–D···A angle, default 30°), within the atom set, between the atom set and the rest, or between the atom set and water, with a minimum occupancy filter. Double-clicking a row selects its atoms and goes to a frame where the bond exists.

• Contact / distance map: contact frequency, mean CA–CA distance, or the change in contacts between the two halves of the trajectory, for the residues of the atom set (contact cutoff, default 4.5 Å). Clicking a cell selects the two residues.

• Interaction energy: Coulomb and Lennard-Jones energy between the atom set and a partner group (the rest of the system, with or without water and ions, or a selection), with the MM charges and parameters of the system.

• Electron transfer pathways: the Pathways model (Beratan and Onuchic): the best donor-to-acceptor path through covalent bonds, hydrogen bonds and through-space jumps, and its coupling along the trajectory.

Dynamics

• Principal components (PCA): frames are superposed on their average first; the variance of each component, the projections on PC1 and PC2, and buttons to animate a component or color the atoms by their weight in PC1 (Figure 2).

• Cross-correlation (DCCM): Cij = <Δri·Δrj> / sqrt(<Δri2><Δrj2>) after superposition, as a heat map.

• Clustering: GROMOS clustering (Daura et al., 1999) on the pairwise RMSD after superposition (RMSD cutoff, default 1.5 Å).

• B-factors and average structure: RMSF, isotropic B = 8π2/3 <Δr2> and anisotropic U tensors, plus the average structure; the B-factors can be exported in a PDB file.

• Quasi-harmonic entropy: quasi-harmonic frequencies and entropy from the mass-weighted covariance (Andricioaei and Karplus, 2001) and Schlitter's bound. It needs many more frames than three times the number of atoms.

• Side-chain rotamers (chi1, chi2): the side-chain dihedrals of the residues along the trajectory.

• Diffusion (MSD): mean square displacement of the water oxygens or of the atom set, over time origins and with periodic jumps removed; the diffusion coefficient comes from a linear fit, MSD = 6Dt. Set the time per frame for D in physical units.

Statistics

• Statistics of a series: mean, standard deviation, block-averaged standard error (Flyvbjerg and Petersen, 1989) and running mean of any series produced by the other analyses, or loaded from a file (columns x y), optionally discarding the first part as equilibration.