Re: [AMBER] facing problem in 3DRISM

From: Tyler Luchko (Lists) <"Tyler>
Date: Fri, 28 Aug 2020 07:26:41 -0700

Hi Angad,

To get rid of the warnings, remove the ‘--entropicDecomp’ flag. You only need this if you want to further decompose the excess chemical potential in to entropic and energetic components. OTOH, if you do want entropic decomposition, you will need to recreate your Xvv file. The one you have is from an older version that did not support entropic decomposition. The warning about this being an experimental feature is out of date.

Similarly, ‘--polarDecomp’ decomposes the excess chemical potential into polar and non-polar contributions and isn’t necessary to calculate binding free energies.

Turning on both entropic and polar decomposition will cause your calculation to take much longer, so only use them if you need them.


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

> On Aug 28, 2020, at 5:27 AM, angad sharma <> wrote:
> Actually I want to calculate the binding free energy of a dimer. And the
> command for the 3drism is as follows
> rism3d.snglpnt --pdb beta-fr1.pdb --prmtop beta10.prmtop --traj
> --buffer 45.0 --closure KH --guv betaAB1 --entropicDecomp --polarDecomp
> --xvv SPC_NaCl.xvv
> it is running properly with some warnings .
> |WARNING> Entropy decomposition is an undocumented, experimental feature.
> |WARNING> Turn off entropicDecomp unless you know exactly what you are
> doing.
> WARNING> Input Xvv file version < 1.000.
> WARNING> Not performing energy/entropy decomposition or temperature
> derivatives.
> I just want to know how to remove these warnings to get correct output.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Fri Aug 28 2020 - 08:00:03 PDT
Custom Search