Hi!
It depends on what type of system do you have and
what is your simulation goal.
For nucleic acids, minimal neutralization salt is OK.
We did few RNA systems and compared
minimal Na+ with excess Mg2+ simulation, and did
not see any really systematic cation effects, on
typical time scales around 25 ns.
Proteins might be different story.
In general, Cl- could cause troubles, anions are polarisable
species and less accurately described by pair additive
force field than Na+.
Others might disagree, but I prefer minimal salt and
well tested Na+, for Nucl.Acids.
Jiri
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> Dear Amber users,
> I was wondering what happens of we use extra sodium
> and chloride ions during Molecular Dynamics ( meaning
> use some particular salt concentration)?
> Is it necessary? What difference does it make?
>
> Happy Holidays!!!!!!
> Thanks a lot in Advance,
> Varsha Gupta
>
>
>
>
>
>
>
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Received on Sat Dec 17 2005 - 01:53:00 PST
