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

From: Fabian gmail <>
Date: Wed, 4 Nov 2015 18:21:40 +0200

I have a related question:

I want to simulate a drop of acetone + water +drug which actually will have millions of water + acetone molecules, that cannot be simulated explicitly of course, so are there models for implicit for mixed acetone + water solvent? Or can that be produced?

I would like to compare the behaviour of several drugs in pure water vs water + acetone, again implicit model.

Thanks a lot in advance,


Dr. Fabian Glaser
Head of the Structural Bioinformatics section

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL

fglaser at technion dot ac dot il
Tel: +972 4 8293701

> On 4 Nov 2015, at 1:12 PM, Carlos Simmerling <> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
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Received on Wed Nov 04 2015 - 08:30:04 PST
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