[MMTK] problems with molecular dynamics

[Konrad Hinsen]

"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.
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