Dear LAMMPS users,
Suppose we have a graphene sheet solvated in water. In LAAMPS, how can we measure the average distance of water molecules within 0.3 nm above the graphene surface? And by average distance, I mean the average distance of water molecules from the graphene sheet.
what is the systematic approach that I can take for calculating this quantity?
Thanks in advance,
Ehsan
Dear LAMMPS users,
Suppose we have a graphene sheet solvated in water. In LAAMPS, how can we measure the average distance of water molecules within 0.3 nm above the graphene surface? And by average distance, I mean the average distance of water molecules from the graphene sheet.
for starters, “average distance of water molecules” is ill defined.
you can measure distances between pairs of atoms. but then which pairs?
you can also measure the distance orthogonal to a plane (easily if if the plane is aligned with the cartesian coordinate system). but is this really a giving a good representation of the situation?
and what is the reference point for a water molecule? the oxygen atom, the center of mass? or any atom?
what is the systematic approach that I can take for calculating this quantity?
The most systematic approach that I can think off is not computing a distance, but rather creating a density profile for each, the graphene sheet and the water molecules. if needed also separately for hydrogen and oxygen.
When computing an average, your results would strongly depend on what you use as cutoff for distances to be considered. It would be more consistent to provide the most probable distance.
axel.