My idea is that you could get a qualitative view of the possible
range of motion of your system to get a feel for how much of it
the solvated md was covering. I don't think I would do more than
watch the movie for a few minutes and maybe grab some interesting
frames for exploratory solvated runs. It's more for creative thought.
Bill
Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, 2014-03-17 at 13:45 +0200, Soumendranath Bhakat wrote:
> > Dear Carlos;
> >
> > Can you please put any scientific article related with your quote " Vacuum
> > dynamics could
> > introduce terrible artifacts"
>
> This should be readily apparent. DNA and RNA duplexes, for instance,
> are inherently unstable and come apart completely in vacuum (see the
> first Amber tutorial for a demonstration). Without solvent stabilizing
> the negative charges of the phosphate groups, the two strands repel each
> other strongly. (Of course, in a vacuum I would not expect the
> phosphates to be deprotonated). Also, the very nature of the
> "hydrophobic effect," which is responsible for protein folding (i.e.,
> the structure of a protein's native state) is driven by solvent entropy
> at room temperature. That in itself is strong evidence that the native
> state of a protein in solution is drastically different from its native
> state in a vacuum. If you look at the papers that introduced the
> Merz-Kollman charge scheme used by most of the standard Amber force
> fields, you'll see that HF/6-31G* was intentionally used to derive
> charges because its neglect of electron correlation overly polarizes the
> charge distribution *similar to what you see in solution*. There is
> anecdotal evidence everywhere and you can see this assumption used in
> many papers even if there is no direct study.
>
> Furthermore, many articles address so-called crystal artifacts which are
> attributed to differences between the crystalline environment and
> differences in solution. The crystal environment, however, is still
> quite close to solution in most respects (it does form in solution,
> after all). Vacuum introduces a far greater perturbation than does a
> crystal, so I would expect vacuum artifacts to be (much, much) worse
> than crystal artifacts.
>
> Long story short: chemistry in solution is _far_ different than
> chemistry in a vacuum or in the gas phase. I agree with Carlos that you
> should avoid vacuum dynamics for studies intended to take place in
> solution.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Mar 19 2014 - 19:30:08 PDT
