Dear all,
I am doing simulation for a polymer/water system. I would like to do RDF and coordination number analysis for this system. I got results like in figure I attached here. I know the trend is correct but I didn’t understand some concepts. As shown in figure, l=5 (lambda) is the lowest water content and l =25 is highest. First: why increase in water content lead to decrease in height exactly? I can not understand this behavior.
Second: As we know, in the distance of first minimum of RDF we can obtain coordination number of first hydration level. on the other hand coordination number is Integral of RDF. But in the highest hydration level we have lowest area under RDF plot and we expect lowest CN but CN is the highest. Why?
Thanks alot in advance
Hi,
Your post is a little vague to be able to give good feedback on. What is CN?
Anyway, is your polymer hydrophobic, or alternatively, does it have more affinity for itself compared to water? If so, maybe it is clumping together and excluding water. This would explain the decreased RDF between water and the polymer. Just an idea. Again, too few details to give better feedback on. Visual inspection of the system can also be helpful
Hi John H Dupuis
Thank you very much for your response.
CN is coordination number. we can specify number of water molecules using distance of first minimum. For example, black line shows there are 5 water molecule in first hydration shell. I read a similar article said that :
RDF peaks are observed to decrease in height with increasing
hydration level which could be attributed to the stronger
solvation effect of water molecules on the sulfonic acid groups
at increased levels of hydration.
I can not understand solvation effect of RDF peak height variations.
Article link:
https://www.academia.edu/28803565/Molecular_dynamics_simulation_analysis_of_hydration_effects_on_microstructure_and_transport_dynamics_in_sulfonated_poly_2_6_dimethyl_1_4_phenylene_oxide_fuel_cell_membranes
Thanks again for your help.
I think you are missing the factor of bulk density here. The CN is equal to
4 * pi * rho * int[g(r) r^2 dr] for the first shell, where rho is the bulk density. If in your simulations the bulk densities are different, it can explain the discrepancy.
Consider also the fact that the integrals 4 * pi * rho * int[g(r) r^2 dr] over [0, R] should be number of particles within radius R of a reference particle. If the system was homogeneous, one would expect the integrals int[g(r) r^2 dr] to be N / (4 * pi * rho) ~= V / (4 * pi) and the same in the three cases, but that's definitely not the case in your plot.
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