The Analysis mode of MobyWat compares the positions of water molecules of a reference structure with positions of water molecules from a molecular dynamics calculation. Commutability, mobility, and occupancy are calculated for all water molecules helping an assessment of quality and stability of their experimental positions. Success rates are also calculated to estimate the quality of water positions from simulations.

Commutability. During a time period, a water molecule can either remain at its starting position or be replaced by other water molecules. Commutability tells how many water molecules of different identity would be capable for such a replacement by coming close to the position of the reference water molecule during the simulation time and the result is printed for each reference water molecule into a text file. Note that in the present version of MobyWat there is no maximal distance limit defined for the closest water molecules, the distance matrices include all distance values calculated.

Mobility. For each replacing water molecules, the frequency of their occurrence during the simulation time is calculated, expressed in trajectory % and printed into a file. High frequency values correspond to low mobility of a replacing water molecule. Low commutability and mobility values may hint that a reference water is conserved.

Occupancy (residence, match). The occupancy value shows how often any water molecule approached the spatial position of a reference water molecule during the time period of the trajectory. The user can set a maximal distance tolerance to define a successful approach. Occupancy values are listed as trajectory % for all reference water molecules into a separate text file. Note, that in contrast with commutability and mobility, occupancy does not account for the identity of the water molecules selected from a frame. Large occupancy value of a reference water position shows that the position is well-defined and its spatial location is probably correct and/or conserved.

Success rate. Success rate quantifies the match between water positions produced by a simulation method and reference positions. The calculation is performed for all (nth) frames of the trajectory (Eq. A1) without clustering of the frames.

Eq. A2   Eq. A1


A detailed User's Manual and test package for Analysis mode can be found on the Download page

Analysis mode has been tested for calculation of success rates. Other parts are under test and development.