From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 01 2012 - 07:37:18 CDT
On Tue, May 1, 2012 at 3:50 AM, Boyang Wang <pkuwangboyang_at_gmail.com> wrote:
> Hi Raghav,
>
> 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.
what the hell is that supposed to mean?
where is the relation to the question of
the original poster?
what has quantum mechanics to do with the
technical problems of getting topology building
tools to work as expected?
axel.
>
> Best,
> Boyang
>
> 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
>>
>> Raghav
>>
>>
>
>
>
> --
> Boyang Wang, Ph.D.
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:29 CST