Hi everyone!!
I perform the MD simulations on adsorption of a Ligand on Graphen nanosheet.
I want to calculate Relative concentration profiles of water around Graphen. Any idea how gmx post processing tool execute it?
#gromacs # Relative concentration profile
This may not be exactly what you're looking for but you could also use "gmx rdf" to get an idea of the different "densities" of molecules surrounding your graphene. I've used it to show the accumulation of certain molecules and depletion of others around a drug I study.
I've attached a picture of a simplified RDF plot. Essentially, anything below one means that molecule is depleted at that radius from the reference. Anything above one means that the molecule is enriched.
So, when we look at the plot we can see the molecule 1 is much more enriched than molecule 2 at around 1 nm.
Note: This rdf was made in ignoring one plane. Normally, we'd expect them to start at zero due to London repulsive force, but in this case they can overlap in the planes we're measuring causing it to be non-zero at very low radii.
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