Umbrella Sampling Browser

An umbrella sampling run leaves dozens or hundreds of windows on disk. WHAM turns them into a free energy profile, but it does not tell whether the windows were good: whether neighbouring windows overlap, whether each window stayed near its target, whether the run is long enough. Analysis > Umbrella Sampling Browser... answers those questions and lets you load the structures of any window, a range of windows, or a path on a 2D PMF as objects in EasyHybrid (Figure 1). A complete walk-through is given in the tutorial Checking and exploring umbrella sampling runs.

Opening a run

Load (or keep) the system whose atoms the windows hold, open the browser (or press Browse Windows... in the WHAM window) and choose the folder of the run with Browse.... The browser shows what it found: dimension, number of windows, temperature, number of restraint samples and frames per window, and the definition of each reaction coordinate.

• System: the system that receives the loaded frames (it must have the same atoms).

• Coordinates: data collection, equilibration, or the initial structure of each window.

• Stride: read every n-th frame of each window.

• PMF: a PMF file written by pDynamo's WHAM (wham/*_pmf.log), or a WHAM computed by the browser from the restraint data.

• Energy: kJ/mol or kcal/mol.

Views

• Windows: Window map, with the windows colored by a property (for example the deviation of the mean from the target, in units of the restraint width).

• Diagnostics: RC distributions and overlap, Overlap between neighbours, Mean RC against the target, RC along the run (selected windows) and Coverage of the RC space (2D).

• Free energy: PMF and windows and Convergence (WHAM by halves and by blocks of the data).

Each view has a table and a Details tab that explains the numbers; Export Image... and Save Table... save them.

Selecting and loading windows

Click windows in the map, or near a window on the PMF, to select them; the order of the clicks is the order of the resulting trajectory (Clear, All, Row, Column and Range help with 2D runs). Then load them as One object per window, One trajectory (windows in order) or Representative frames (one per window), or Export... them to a file (.dcd, multi-frame .xyz, or one .pdb per frame). Double-clicking a table row loads that window.