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

From: Fabian gmail <>
Date: Thu, 5 Nov 2015 10:51:13 +0200

Thanks for the answer.

Maybe I am wrong but the calculation of a drop of acetone of a drug disolved in it gives me this number, anyway I will rephrase my question. I would like to simulate the process of dissolution of a drug from pure acetone into a water + acetone mixture when a drop of this acetone pure +drug is dropped in pure water. How should I do that?

I thought about the following procedure:

1) Run relatively short simulation of one or two drug molecules in pure acetone (I thought about a drop from that comes millions, but maybe I really can use a large box).

2) Put this stabilised equilibrated pure acetone + drug mixture into a larger water box, that wil contain the acetone + drug like a drop. Is that step OK?

3) Run all this mixture drug + acetone + water environment and simulate the drug + acetone diffusion into the water environment, and hopefully learn about the precipitation process. The drug in this way should form nanoparticles, and this is the experimental process.

4) Do the same with other drugs and drugs mixtures that are given together.

The objective is to give insight into the process of disolution and nano precipitation of the drugs from acetone into acetone + water (acetone slowly evaporates in real experiments).

Is that a good approach?
A better idea?

Any hints will be appreciated. I found this paper but they use GROMACS coarse grain model… I want to stick with amber. <>

I have done the simulation of those drugs in pure water, but this is not very helpful, since they just cluster as expected, since they are highly hydrophobic, I am hoping that using acetone will teach me about the precipitation process as it really occurs. If I see differences in energies or kinetics or anything using two different drugs it wil be very useful to guide experiments.



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 8:07 PM, David A Case <> wrote:
> On Wed, Nov 04, 2015, Fabian gmail wrote:
>> 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?
> Why do you need "millions" of water and acetone molecules? How many drug
> molecules do you expect to have in any single simulation?
> It's not hard (or all that expensive) to simulate mixed liquids, and using
> thousands of solvent molecules is generally quite accurate.
> If you really need an implicit model, check out CosmoRS.
> ....dac
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Received on Thu Nov 05 2015 - 01:00:05 PST
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