What sort of sampling method did you use? What water model? If you
did not sample sufficiently, then you simply aren't observing enough
simulation to tell. How did you sample (REMD, long simulation, etc.)?
Whenever possible, you should validate any modeling method against
experimental data that correlates to the sort of simulation you are
doing. Are there no experimental studies at all to use for
comparison?
It is possible that the behavior you see is indicative of natural
behavior, though I doubt it is a perfect reflection. If there are
deviations, I would expect them to be related to the absence of
polarizability in the model.
:-) Lachele
On Tue, Oct 5, 2010 at 6:00 AM, Sergey Samsonov
<sergeys.biotec.tu-dresden.de> wrote:
> Dear All,
>
> I've been checking, how the flexibility of some saccharides changes (in
> terms of glycosidic linkages dihedrals) depending on ionic strength.
> What I found is that there are neither quantitative, no qualitative
> differences for the effect of ionic strength in the range I used (from 0
> up to quite extreme 5M for NaCl). Do you think this could be explained
> by real physical nature of sugars flexibility or it is rather the force
> field (I used ff03 + GLYCAM06) inability to find such effects as changes
> in flexibility of molecules (or their diffusion constant, which I also
> checked) under different values of ionic strength in solvent?
>
> Thanks in advance and best regards,
>
> Sergey
>
>
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Oct 05 2010 - 07:00:07 PDT
