Hi Joy,
Can you provide more information? A plot comparing of the RDFs would be useful. As would details on the solvent and the expected and obtained results.
A couple of things to think about:
1) If the isothermal compressibility is negative, you have an unphysical solution. You will typically see long range oscillations in the RDF when this happens. Using a larger LJ radius can help get a physical solution.
2) For accurate solvation free energies, you will need to apply a correction. In AmberTools 16 you can specify parameters for the Universal Correction or ask that the PC+ correction be applied to 3D-RISM output (but not rism1d). While some recent work has had success applying PC+ to non-polar liquids, I have had poor results in the one case that I have tried.
Hope this helps,
Tyler
> On Sep 1, 2016, at 12:21 PM, Jingyi Yan <jyan7.ualberta.ca> wrote:
>
> Hi All,
>
> I am modelling a non-polar solvent for amber 1d-rism calculation. With a
> set of parameters for sigma and epslon, I got a convergent solution for
> this model. But when I compared the solvation free energy of this model
> with its experiment data, there is a big difference. And for the radial
> distribution function, the result from 1d-rism calculation is far from
> all-atom simulation data and experiment data.
>
> Any advice is appreciated!
>
> Best,
> Joy
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Received on Thu Sep 01 2016 - 13:30:03 PDT
