We haven't found that any of the implicit models do very well with
oligosaccharides. My best advice is to try them all and see which one best
models the systems of interest to you. If any comes close enough for your
needs, then use it. You'll need to include this validation in any papers
you publish about the work.
On Sun, Jul 24, 2016 at 8:58 PM, yunshi11 . <yunshi09.gmail.com> wrote:
> Hi mailing list,
>
> I'd like to run MD for a polysaccharide and check how stable some
> inter-residue interactions are. Due to limitation of computational
> resources, I am thinking of using implicit solvent with Glycam force field.
>
> Would this significantly undermine the accuracy since polar interactions
> between sugar hydroxyl groups and water molecules are no longer modelled by
> implicit solvent? Is there another way to get better accuracy and
> performance with limited resources?
>
> Thanks for any suggestion.
>
> Yun
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sun Jul 24 2016 - 19:30:02 PDT
