Re: [AMBER] How to choose between implicit and explicit solvent

From: Carlos Simmerling <>
Date: Wed, 4 Nov 2015 06:12:06 -0500

It depends on the needs of the project. I use both in my lab. When you need
a solvation free energy instead of enthalpy, implicit solvent does that
(MMPBSA for example). Another reason to choose implicit might be that the
system is not globular (for example, very long DNA, or fully extended
protein) and would be hard to fill a periodic shape with explicit water.
Another reason is that implicit solvent has low viscosity, so global
dynamics can often be faster compared to explicit water.

However, the calculations scale differently with number of atoms, and
implicit solvents tend to have lower accuracy that explicit solvent.

So overall, there is a speed/accuracy tradeoff and your project needs
determine which is best.

On Wed, Nov 4, 2015 at 4:15 AM, Jean-Patrick Francoia <> wrote:

> Hello,
> I have a simple question regarding the choice of the solvent: implicit
> or explicit.
> What are the general recommendations for choosing ? There are many
> tutorials or publications comparing explicit and implicit solvent, but
> there is no general explanation on how to choose.
> Regards
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Received on Wed Nov 04 2015 - 03:30:03 PST
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