GROMACS version: 2016.4
GROMACS modification: Yes/No
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Hello users,
I want to have surface maps/ contour maps of the density profiles. Basically, I want to have my clay surface underneath and map the movement of ions (density) above the surface at a specific distance from the clay surface. The clay surface underneath should show a square grid, say 3*3 nm containing a series of hexagonal cavities (formed by the surface oxygens) are fixed and the Cs cation is mobile and I want to plot the contour map of it.
I tried using the option densmap, but it gives me heatmaps and I am not able to superimpose it on the clay surface to have a better understanding of the specific position of Cs on the clay surface. Is there any way in which I can get a contour plot of the same?
Thanks in advance,
Deb
