User manual

File upload

File Picker

Press "Choose files" and select appropriate HILLS files. Multiple files can be selected with usage of Ctrl or Shift key.

Drag and drop

Drag and drop chosen files into the empty center of the program area. Multiple files can also be used.

Examples

For demonstration purposes several example HILLS files are included in the program. Any of them can be picked by clicking on "Examples" button and selecting an example. More information about the simulations are in the accompanying article.

The program accepts HILLS files produced by Plumed 1.3 or Plumed 2.x. Syntax of files are recognised automatically, nothing has to be manually adjusted. Gaussians written in HILLS files are being sorted according to time (in the case of Plumed 1.3 files) or timestamp (Plumed 2.x). For disabling sorting, sort=false has to be written into the address line (see further).

Controls buttons

Languages  

Button located at right top corner controls a selection of languages. At the current version of the program only English and Czech languages are supported.

Play/Stop  

Button located at left bottom corner starts or pauses visualization of the data.

Reset

Returns the vizualization to the beginning.

Measure

Opens a window with tools for measurement of energy and other quantities (see further).

Speed

Sets the speed of visualization. Normal speed (1x) is adjusted to make the whole visualization last approximately 10 seconds. Speed could be limited if the computer is not powerful enough for chosen resolution and speed.

Resolution

Sets the size of the free energy matrix, where potential is deposited. This resolution does not affect the resolution of the image, but it improve quality of the energy surface.

Export

Opens a new window for image export. For more information see "Image Export" category.

Loop

If it is turned on, the visualization will not stop at the end. Instead iit will loop back to the beginning.

WebGL

Turns off or turns on the usage of WebGL technology. WebGL is much more effective for visualization, but it may not work properly on some devices. Devices without WebGL support have WebGL disabled regardless the value of this button.

Resize

By holding left mousebutton over this button it is possible to change the size of the program screen. If size of the plot area is close to square dimensions, size will be adjusted to exactly square one.

Slider

Control element above the bottom control strip. It displays the current progress throught the visualization. Moreover, the progress can be changed by moving the slider to either side.

Zoom

Zoom

Zooming in and out of the plot is done by mousewheel. Position of mouse over the plot does matter, because zoom is focused to that point.

Panning

When zoomed in, the focused area can be moved by pressing right mousebutton and draging. It is impossible to move outside area with ploted data.

Axis adjustment

CV name

Collective variables can be renamed by clicking on the axis title and by writing a new name.

Energy axis units

Units displayed on the energy axis can be changed by clicking on them. There are two possibilities: kJ/mol and kcal/mol. The program cannot recognize appropriate units from HILLS file, so it has to be set manually.

Image export

Save image

After click on the Export button, the whole visualization is replaced by an image that can be downloaded through right click and SaveAs.. action.

Image resolution

It is not possible to select dpi value for the created image but you can increase the resolution by increasing the size of plot (Resize button).

Exported image is exactly the same as the visualized plot, so any custom changes (e.g. change of axis name) must be done before the export.

Measuring

Options described below are accessible when Measure button is on (see above).

Free energy and CV coordinates

Pointing with a mouse cursor on any point in the plot will display corresponding CV coordinates and free energy value.

Free energy difference

Pressing the left mouse button and dragging to another point will display energy difference between these two points.

Closest hills

Clicking on any point of interest on plot will display three hills which are closest to selected point in the CV space. Hills are displayed in the form of time records, so they can be used to find related frames in a trajectory file.

Advanced controls

Many settings can be control via buttons. Moreover, all of them and several others can be changed by modification of URL in the address line. Each non-default settings is written there and separated by & character. Only non-standart settings will be described further.

Tests

tst=1 - runs pre-prepared tests for evaluation of the program. Every test should pass, but failing in any of them do neccesary mean that the visualization won't work.

vtst=2 - runs pre-prepared benchmarks for evaluation of the program. Benchmarks was prepared in such way that all produce 100 points on author's PC. Values less than 20 points could mean that visualization performace is severy hindered.

Log level

log=X - There are several levels of importance for logs starting from level 4 (debug information) to level 1 (error messages). Only messages whose level is less or equal to the log level settings will be displayed. Thus log=1 will display only error messages.

HILLS sorting

sort=false - Turns off automatic hills sorting by timestamps in the HILLS file. Automatic sorting should handle variety of situations (multiple walkers, restarts,...), but in case it fail, turning off sorting could help.