Hello experts,
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?
Thankyou @cblau sir for replying to my query and providing me with the link. Yes, I read the paper. I think this might solve my problem. I will keep you updated and will message you in case I need some more help related to it.
Deb
You’re selecting atoms with the name OB1. Using the “name” keyword doesn’t require an index file, and an index group is only needed if you’re selecting a specific group that has already been generated.
@jalemkul, @cblau okay, got it. But if I want to use a specific set, say ob, (which contains 1632 atoms as created in my specific index file, random.ndx), what should I write in the -select option of my previous command?
@cblau, My index file has ob containing 1632 atoms, (OB1 OB2 OB3… till OB20), these are basically the surface oxygens that I want to set as a reference for the surface maps and plot the movement of Cs atoms on top of it.
And, when I even try to provide the details of all the atoms of my interest individually, (OB1, OB2, OB3…till… OB20, as mentioned above), I still get no atoms when I visualize it in VMD.?
Hm, you should be able to see a density here - choosing an isosurface representation might help. The 0 atoms are not an issue, as there is no longer the notion of atoms in that density. If that does not work, feel free to share your input files with me in some way and I’ll check what goes wrong on the maptide side.
