[gmx-users] GMX Density – Setting Start and End Position Along Z Axis

[ALEXANDER DHALIWAL]

Hello:

I am attempting to use the gmx density function to calculate the electron
density of a bilayer system with and without a solute. In order to do this,
I must calculate the density of various elements (i.e., lipid head groups,
lipid tails, solvent molecules) along the bilayer normal (z axis) for both
a pure bilayer system that I have run and a similar one containing the
solute, and then I must find the difference between the respective electron
density profiles. However, each system has slightly different box
z-dimensions, so the two instances of running the gmx density command
result in differently spaced intervals along the axis. This makes it hard
to compute the difference.

Is there a specification by which I can choose the starting and ending
place along the z-axis for my density calculation, such that I can have
even intervals spaced at the same places for both of my calculations? I
have tried changing the number of slices to approximately accommodate for
the differences, but it still isn't working. Any help would be appreciated.

Thanks!

Alex