On Sun, Aug 16, 2009, Catein Catherine wrote:
>
>
> Should I do neutralize the charges in DNA-protein complex with Na+ or
> Mg2+ (before adding solvent) when we generate the prmtop or inpcrd
> files? I found Na+ was used in the tutorial, but some paper used Mg2+,
> why?
This choice almost always has to do with the sorts of experimental conditions
that were used in studies to which the calculations will be compared.
...dac
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Received on Wed Aug 19 2009 - 22:44:41 PDT
