Hello,
Is there a software package to study the effects of the structured solvation shell around solutes in aqueous solutions? I am trying to 1)quantify the loss of entropy upon addition of a solute to water. 2) quantify the number of water molecules that would be kinetically restricted in the solvation shell around the solute.
Thank you
OPLS has some interesting features. See the work by Michel et al on JAWS.
You can right your own code, using coordinates from simulation trajectory or can do initial analysis in CHARMM/gromacs.
In the beginning, it is necessary to make a model of substance , either manually, or by means of some force field generator, for example:
GAFF http://ambermd.org/antechamber/gaff.html
Automatic FF generator http://www.biomolecular-modeling.com/FF/index.html
FFTK http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/
Simulations can be performed in any suitable package
https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling
Many packages have tools for analyzing trajectories (for example Tranal http://www.fos.su.se/~sasha/mdynamix/) or a scripting language on which you can write your own.
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