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,
Fabian
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
http://bku.technion.ac.il
> On 4 Nov 2015, at 1:12 PM, Carlos Simmerling <carlos.simmerling.gmail.com> 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 <
> jeanpatrick.francoia.gmail.com> 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
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 04 2015 - 08:30:04 PST
