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

From: Fabian gmail <>
Date: Thu, 5 Nov 2015 14:45:45 +0200

Sorry I didn’t explain myself well enough.

Just to clarify, I have two different drugs (drug1 and drug2 and their combination also), each of them can be grown into pure drug nanoparticles which include millions of molecules of drugs each (I don’t know how many)…. each nanoparticle is about 50-150 nm in size and includes ONLY pure drug.

So two different drugs form nanoparticles of different sizes, starting from pure solution of acetone + disolved drug1 or drug2 or both, and then acetone + drug are dropped into water bulk, is this process precisely I would like to investigate….

This is the reason I want to make the simulation, and I don’t know how to simulate a drop of acetone + drug1 or drug2…. and then put it into a water box…. within a reasonable size and time. Any hint or paper or idea what is the right way to try would be great. Or if you know who may I talk to also would be great. Maybe I just need to do an approximation, but I would like to get some inputs from somebody with some experience with drugs and MD.

Thanks a lot for your time in any case,

Best wishes,


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 5 Nov 2015, at 2:27 PM, David A Case <> wrote:
> On Thu, Nov 05, 2015, Fabian gmail wrote:
>> 1) Run relatively short simulation of one or two drug molecules in pure
>> acetone...
>> 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.
> Others may be able to answer here...this is well outside my experience. As I
> read your description above, you have "one or two" drug molecules. I'm not
> sure how such a system could form nanoparticles.
> ....dac
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Received on Thu Nov 05 2015 - 05:00:03 PST
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