On Wed, Jun 7, 2017 at 10:07 PM, Dd H <ddhecnu.gmail.com> wrote:
> I ask the question because I wonder why people don't use implicit solvent
> now.
Hi,
People are still using implicit solvent. This really depends on what you
want to learn.
E.g: You can check our paper for protein folding with implicit solvent +
AMBER GPU.
I think explicit solvent MD can not beat that with current computer power
(except Anton from DE Shaw group).
http://pubs.acs.org/doi/abs/10.1021/ja5032776
cheers
Hai
> Thank you for your help. Maybe I should learn more about basic
> knowledge to fully understand your answers.
>
> Best regards,
> Dading Huang
>
>
> On Thu, Jun 8, 2017 at 9:19 AM, David Case <david.case.rutgers.edu> wrote:
>
> > On Wed, Jun 07, 2017, Robert Molt wrote:
> > >
> > > I have a neophyte question with regard to the current thread. Ignore
> the
> > > issue of faithfully representing the electronic environment in implicit
> > > solvation. To what extent can implicit solvation ever be used if one
> > > wishes to describe the entropy of a system? If phase space does not
> need
> > > to be "traversed" with proper sampling, because the electronic
> > > environment "instantaneously" transmits the new proper "field," doesn't
> > > this cause a problem?
> >
> > The continuum model estimates the solvation free energy, which includes
> > both enthalpic and entropic terms.
> >
> > >
> > > I understand, factually, that people use implicit solvation and
> estimate
> > > entropy all the time, but it is not obvious to me what logic allows one
> > > to escape the above issue.
> >
> > When people talk about "entropy" in implicit solvent models, they are
> > almost
> > always refering to the configurational entropy of the solute, whose
> > conformations are being explicitly sampled. Entropy terms arising from
> the
> > solvent are "hidden" inside the solvation free energy term.
> >
> > ...hope this helps...dac
> >
> >
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Received on Wed Jun 07 2017 - 21:30:02 PDT
