Re: [AMBER] Single ion solvation free energy calculations.

From: Tyler Luchko (Lists) <"Tyler>
Date: Thu, 27 Feb 2020 10:07:01 -0800

Hi Akhilesh,

3D-RISM can certainly be used to calculate solvation free energies of ions. To get a sense of the accuracy you can expect, please see

Johnson, J. et al. Small molecule hydration energy and entropy from 3D-RISM. J. Phys.: Condens. Matter 28, 344002 (2016).

You can use the settings from the paper or, if you want better computational performance, I recommend experimenting with the ljTolerance setting that we have added since that paper. It should allow you to reduce the size of the solvation box. Recommendations are in the Amber manual. If you are dealing with larger molecules, you can also look at treecode parameters, but these won’t make much difference unless your solute has at least a few hundred atoms.


Tyler Luchko
Associate Professor
Department of Physics & Astronomy
California State University, Northridge
Northridge, CA <>

> On Feb 26, 2020, at 1:33 PM, Akhilesh Paspureddi <> wrote:
> Greetings!
> I have looked at FEW tutorial for free energy calculations and I could follow through the steps.
> In my work I’m trying to get single ion solvation free energy (or charged ligands binding free energy) and this will need correction terms for finite size effects when the system will have net charge because of electrostatic decoupling. Is it possible to account for these in FEW workflow currently? Or Is there any other easier way to calculate solvation free energy for charged ligands ( like 3D-RISM-PSE approach)?
> Regards,
> Akhilesh
> Graduate student
> UT Austin
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Received on Thu Feb 27 2020 - 10:30:02 PST
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