Re: [AMBER] The 3D-RISM-PC+ information for each atoms

From: Tyler Luchko (Lists) <"Tyler>
Date: Thu, 7 Feb 2019 11:38:29 -0800

The nature of the PC+ correction makes it difficult to assign a contribution from each solvent site. Specifically, the correction makes use of the inverse isothermal compressibility and total density, which are not easily decomposable into solvent site contributions. The same is true of the Universal Correction. For this reason, we don’t report contributions from individual sites.

Also, it is not recommended to to use PC+ with the KH closure, as there are systematic errors. Use the PSE-3 or higher order closure with PC+ or use UC with KH. You can find details of this in

Johnson, J., Case, D.A., Yamazaki, T., Gusarov, S., Kovalenko, A., and Luchko, T. (2016). Small molecule hydration energy and entropy from 3D-RISM. Journal of Physics: Condensed Matter 28, 344002.
Hope this helps,


> On Feb 6, 2019, at 11:49 PM, Eugene huh <> wrote:
> Dear all,
> I'm using the 3D-RISM because of solvation free energy ..etc.
> I got "rism_excessChemicalPotential, rism_solvationEnergy, rism_-TS" for
> each atoms with --closure KH and --gf
> BUT I couldn't get that for each atoms with --pc+. I'd like to know the
> information about each atoms with 3D-RISM-PC+ (If I put on "--pc+" option,
> print out just "Total")
> Can someone tell me, how can I get the information for each atoms with PC+ .
> It is my option comment:
> rism3d.snglpnt --pdb ../../min.pdb --prmtop ../../A.prmtop --closure KH
> --cuv All_RE_300_c --huv All_RE_300_h --uuv All_RE_300_u --xvv
> ../..All300_6.xvv --chgdist All_RE_300 --gf --pc+ --uccoeff
> 0.008,-0.00053,-3.2,0.010 --centering 1 --entropicDecomp --polarDecomp
> --verbose 2 >> run3drism_All_RE_300.out &
> Thank you
> ᐧ
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Received on Thu Feb 07 2019 - 12:00:02 PST
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