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 Mon Sep 05 2011 - 14:00:04 PDT
