In article <EMKsb.877$fg2.20045 at news.xtra.co.nz>, "jacjentait" <jacjentait at xtra.co.nz> wrote:
> I don't know if this is the correct forum but here goes ,
>> Every molecular program i have seen has visuals that show molecules as beads
> or shapes floating in "space" .
>> What is the "space" ?
>
If a single protein molecule is being simulated, the simulation is
considered to be in vacuo, and the space is 'nothing'. However (there's
always a however, right?), specific simulated water molecules can be
added to the calculation, and/or a continuum model of water can be used,
and/or a simulated dielectric constant can be included in the
calculation.
I'll stop there to keep it short.
cheers,
Marj
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