From: Boyang Wang (pkuwangboyang_at_gmail.com)
Date: Tue May 01 2012 - 02:50:35 CDT
you can use quantum mechanics to solve. In the solution, variational method
will find global energy minima (when it converges). The total charge should
consider the solution. Hope it helps.
On Mon, Apr 30, 2012 at 5:55 PM, raghav singh <raghavbioinfo_at_gmail.com>wrote:
> Hi All,
> I have a question about total charge of nucleic acid system... no matter
> what I have tried it does not sum up to an integer value... for a double
> stranded helix of 24 bp ...i is like 45.9999 ......!! something like this
> (with terminal patch).
> during ionization it tells me that I have to add 46 ions to neutralize the
> system... but it come up with some positive value?
> while if I understand it right it should be -48 with terminal patch or -47
> with terminal patch. (gromacs, amber ).
> and after solvation and ionization it comes up with some positive value of
> 1.23446 ... !!
> if someone have any idea abt it.. please tell me how can solve this one.
> Thank You
-- Boyang Wang, Ph.D.
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