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 - 05:30:04 PST
