Ok, thank you for your answers. My problem is that I haven't a solid
background to judge my work.
Could you advice some papers to increase my general knowledge of
mechanic molecular modelling ? (Not too much maths please, just general
knowledge).
Le 04/11/2015 14:27, Carlos Simmerling a écrit :
> yes these things are less accurate. I would suggest looking a review papers
> on implicit solvent models, as well as some recent applications. Keep in
> mind that there are a variety of implicit solvent models too, and they also
> have speed/accuracy tradeoffs. The choice of which to use for
> postprocessing hundreds of snapshots may be quite different than the more
> approximate ones needed to do billions of time steps of MD.
>
> On Wed, Nov 4, 2015 at 8:18 AM, Jean-Patrick Francoia <
> jeanpatrick.francoia.gmail.com> wrote:
>
>> 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 ?
>>
>> Sincerely
>>
>> 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 <
>>> 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
>>>>
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Received on Wed Nov 04 2015 - 06:00:07 PST
