On Fri, 2012-03-30 at 12:39 -0400, David A Case wrote:
> On Fri, Mar 30, 2012, 板凱哲彦 wrote:
> >
> > vlimit exceeded for step 0; vmax = 29909.5926
> > partition error in shake on processor 0
> > this processor has atoms 1 through 9100
> > atom 9098 is within this range
> > atom 9101 is not within this range !
>
> This is a known (but rather rare) bug. Jason should(!) have recognized this,
> since he wrote a routine in his new parmed program to fix it.
Ah, yes, this is another possible explanation (probably the correct
one). Can you try running your system with pmemd? pmemd will actually
check for valid MOLECULE definitions (and segfaults when NATOM !=
sum(ATOMS_PER_MOLECULE)). I didn't recognize the error message since I
had only investigated these issues with pmemd where the error reporting
is more complete.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 30 2012 - 11:00:05 PDT
