Hi Case,
Thanks for the suggestions. I am working on fixing it, but I still couldn't
find anything. I will ask you again if I cannot fix it at all in the next
few weeks.
Thanks again!
~Surma
On Mon, 5 Sep 2011 08:51:58 -0400, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Sep 03, 2011, tsurma.umich.edu wrote:
>>
>> I have attached the mdin file, coordinate file and prmtop file. Also, I
>> have attached extra_pts.f code which I extended to account for the two
>> extra points in CN- ion.
>
> OK: I hadn't remembered that you were working with a modified version of
> sander. It's not clear how easy this will be to fix, since it seems to
> work for one CN. First, you might keep the extra points, but set their
> charges to zero, and see if that helps the SHAKE problem. Try to follow
> the code to ensure that SHAKE is doing exactly the same operations on
> the second CN that it is doing on the first one. Since the first SHAKE
> seems OK and the second one fails, at some point there has to be
something
> different....
>
> I'm travelling right now, and have limited time to look at this. Maybe
> someone else on the list can spot something in the code that looks funny.
>
> ...good luck...dac
>
>
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Received on Tue Sep 06 2011 - 09:00:03 PDT
