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My main aim is to extract the SWAXS spectra for the hydration shell surrounding a solvated molecule and I am unfamiliar with the idea of excluded solvent volume. I tried looking online but many articles did not elaborate on the process of setting up such a calculation, or directly used an online server for those results.

In my case I have a single large solute molecule fixed and frozen at the center of the simulation box and I can calculate the SWAXS spectra of the entire simulation system using the xyz coordinates. Using this a stepping point, how can I go about calculating the SWAXS spectra for the hydration shell defined by distance cutoff criteria?

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  • $\begingroup$ I gave my +1 long ago, but just came back to see how things were going. It's been a while and this question didn't get any comments or edits since its first hour. Do you have any update based on anything you've learned about this question since asking it? $\endgroup$ Commented Jan 14, 2022 at 1:25
  • $\begingroup$ Hi Nike, sorry i couldn't reply earlier. I was busy with some personal stuff. I haven't got any updates on this question. I thought that it would be nice to have different contribution to the total scattering spectra for different solvation layers around the solute, but I guess the required methodology might be too esoteric and/or cumbersome to be used by most people on the site. $\endgroup$
    – mykd
    Commented Jan 15, 2022 at 16:44

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