I want to calculate the structure of water on the surface of non-polar solute (not for bulk system). For this calculation I cannot use radial distribution curve (g(r)) method because there will be a break in the radial symmetry if I consider a shell around the solute and calculate g(r) of water inside that shell. For the particles which at the interface (boundary of the shell) we don't have radial symmetry. I dont want to use angle dependence for these calculations. Are there any other methods for finding the structure?
1. Sorry for the time taken, I seldomly access social networks
2. Does it exist? Water, as almost every other molecule is normally subject to brownian motion at room temperature. In my experience there is not one structure of water, not even of the protein or the complex. It is dynamic and changes over time.
IMHO the best you can expect is either to run a large MD simulation and pick the conformation with lower energy to further optimize it (but this will not guarantee an absolute minimum energy conformation) or try to characterize the "average" behaviour.
The last is most probably what you want. Hence
3. The right answer is a question: what do you want that for? Depending on your ultimate goal, it may be enough to run a GB/SA or PB/SA calculation if you want to measure solvation/desolvation effects, or maybe other kinds of calculations, again, depending on your ultimate goal.
Dear Jose,
Glad to see your reply.
First of all yes the structure of water non-polar solute is a bit different from that of bulk system. If you plot distribution of water around the solute (just upto a certain distance say first shell) then it will be much more enhanced as compared to bulk water. I can see such results in my system but the problem is calculating radial distribution curves is not a correct method because of the breakage of the radial symmetry for the particles which at the interface of the shell you are considering. So i want alternative method.
Hope i am able to convey my problem.
shashank
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