Z-density profile for specifc atom types in a simulation

User discussions
1

GROMACS version:2020
GROMACS modification: No
Here post your question

Hello all,

I am simulating an aqueous salt solution with two exposed surfaces perpendicular to the Z-direction with Gromacs. I am interested in finding the ‘z-density’ of specific atoms in the salt species to compare their distribution with regards to the surface and in the bulk.

Is there a way of doing this with the gmx density or should I be using another program?

Thank you!
Saman

2

Hi,
I think you can try to gmx density with option -d Z to calculate the density along z directory. To have the density a specific atoms group you have to generate an index file contains those atoms. To achieve this you can use gmx make_ndx or gmx select.
\Alessandra

3

Hi,
Thank you for the response. I’ll try this route and report back.
Saman

4

careful with dynamic Z dimension (e.g., constant pressure) and gmx density. Last time I used it, the box was divided up into segments starting from the bottom to the top, so even with centering options in gmx density the tool is probably not giving you what you expect.

5

Thank you for the tip. I’ll consider this when interpreting the result.