Dear all,
I’d like to observe how density varies within the box, therefore could someone please explain how to find density within each of the slices of a simulation box formed by slicing the simulation cell into 1 angstrom-partitions along the z axis?
gmx density: gmx density — GROMACS 2022 documentation.
Dear Sasha,
I tried but couldn’t figure out how to do the partition and determine density, so could you please explain in detail how I should proceed?
To set a specific number of slices use -sl. The default is 50 slices. To get slices of 1 A, use the length of your box in the Z direction in A as the number of slices. To get the density along the z-axis use -d Z.
Thank you Minalde