[MMTK] Triple bonds?

Konrad Hinsen research at khinsen.fastmail.net
Thu Jul 14 05:19:27 UTC 2011

On 13 Jul, 2011, at 15:51 , Christopher Drost wrote:

> of GAMESS that I might install and peek around. Still, I'm surprised
> that what seems like the most basic molecular-mechanics tasks are
> impossible for open-source projects. PyQuante's energy minimization
> system is buggy to the point of nonfunctional and would take several
> days to debug; MMTK does not believe in error handling and instead
> throws Segmentation Faults which I must trace with gdb. The one thing

First of all, if you have a script using MMTK that produces segmentation faults, please send it to me. Please try to make it as simple as possible, and join a list of the version numbers of all dependencies (Python, NumPy, ScientificPython) as installed on your machine, and also tell me which OS and which compilers you use. Segmentation faults are unfortunately specific to precise combinations of all these, which makes them so hard to track down.

To address the more general complaint you make about "open source projects", please keep in mind that much scientific open-source software is written by very small teams (one person in the case of both MMTK and PyQuante) with essentially no financial support. To make better tested code, we'd need to have larger communities, meaning more cooperation (rather than competition) between research groups. This works in some other fields (an example I happen to know is solid-state physics, where tens of research groups collectively maintain simulation software such as ABINIT using a sophisticated testing infrastructure), but not in biomolecular simulations, for whatever reason.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net

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