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

From: Jean-Patrick Francoia <>
Date: Wed, 4 Nov 2015 14:18:07 +0100

Ok, a lower accuracy. But I meant, does it have something to do with the
kind of interactions between the molecules ?
Let's imagine two molecules interact through hydrophobic interactions,
does the type of solvent matter ? What about hydrogen bonds ?


Le 04/11/2015 12:12, Carlos Simmerling a écrit :
> 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 - 05:30:03 PST
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