there are some books
Understanding Molecular Simulation by Smit
Molecular Modelling: Principles and Application by Leach
plus lots of online resources if you look around.
On Wed, Nov 4, 2015 at 8:47 AM, Jean-Patrick Francoia <
jeanpatrick.francoia.gmail.com> wrote:
> 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 - 06:30:05 PST
