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The Box Density Analysis tool computes the mass density of the periodic box, in g/cm3, for each frame of a trajectory: the total mass of all atoms divided by the volume of the cell. It is used to check the equilibration of simulations at constant pressure (NPT), in which the volume of the box changes along the trajectory. The trajectory must carry its cell for every frame, as the NPT trajectories of the Leap Frog integrator with pressure coupling do.
To open the tool: Main Menu > Analysis > Box Density Analysis (Figure 1).
System / Object: the trajectory.
Frames from / to and Step Size: the frame range (to = -1 means the last frame) and the interval.
Log file: the file where the volume and density of each frame, and their average, standard deviation, minimum and maximum, are written.
Plot the result: plots the density against the frame number, with the mean as a dashed line (Figure 2).
In Figure 2 the density of a solvated chignolin box starts at about 1.0 g/cm3 and fluctuates around 1.04 g/cm3 after the first frames of a 10 ps NPT simulation (300 K, 1 atm).
Figure 1: The Box Density Analysis window.
Figure 2: Density of the box along a 10 ps NPT simulation of solvated chignolin.
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