[MMTK] problems with molecular dynamics

michael.l.stoppelman.1 stoppeml@purdue.edu
Mon, 11 Nov 2002 12:31:59 -0500 (EST)


I figured out why it core dumped on my cygwin install. I had installed
Scientific Python before NetCDF, it was core dumping in the C
when it looked for the Scientific Package in the trajectory code.

-Mike



On 8 Nov 2002, Konrad Hinsen wrote:

> "michael.l.stoppelman.1" <stoppeml@purdue.edu> writes:
>
> > My first idea is to extend the PeptideChain class adding a addResidue
> > method.  After every addition to the PeptideChain I want to minimize the
> > energy over that chain. I attempted to do this with only two residues and
>
> Sounds like a good approach.
>
> > But first, I wanted to see if any of this would even work:
> ...
>
> > that code core dumps.
>
> It works fine on my system. There is certainly nothing wrong with your
> code, in fact, you should never get a core dump unless you write your
> own C code. In practice, you can crash Python in rare cases by using
> too much memory, but that's all I am aware of. I don't know of any bug
> in MMTK that would cause core dumps, although of course I certainly
> don't know all bugs!
>
> This seems to be a machine-specific problem, so I can't do much
> directly. Can you check with a debugger where the code is crashing? If
> it is in the minimizer, could you try a simple energy evaluation first
> to see if that works fine? And try the conjugate gradient minimizer
> for comparison?
>
> Konrad.
> --
> -------------------------------------------------------------------------------
> Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
> Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
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