On Wed, Oct 10, 2012 at 10:41:52AM +0200, David van der Spoel wrote: > On 2012-10-10 10:30, Noel O'Boyle wrote: > > > > What is the link between Gaussian files and Gromacs? Or is this a > > separate issue? I would have thought that Gromacs has the complete > > structure with bond orders and explicit hydrogens. If so, it could > > read the Gaussian file and set this information based on that (in > > general, the atom order is preserved on reading/writing with OB). > > > > - Noel > > > This is for generating topologies based on Gaussian calculations. Since > one only has element names and coordinates and overall charge in such > files it would be handy to use OB to extract bond orders.
OB also has an atom typing facility which allows to find their types and map them between different forcefields, tough I haven't looked into details of those. At some point I wanted to use those for generating Gromacs topologies, but found that the fragments I put together already had explicit atom types, so just reused those in topology with a little bit of Python scripting. > > Geoff was mentioning that the API would have to change to support this, > but in fact it says in the OB documentation that all info is extracted > from the input file, and reading the charge from a gaussian file could > be used in OB internals without changing API I would expect, but I'm not > familiar with the API yet. Yes, all information is extracted from the files to the extent developers have implemented it. So for file formats with lot of information there might be actually read only subset of it, but usually it is just a matter of improving the particular filetype plugin which doesn't change ABI/API. In case of Gaussian format, AFAICS it reads total charge, Mulliken, ESP and Natural Population charges and one can choose to use any of those. > > In general open babel is useful for file conversion as well, so gromacs > could use it for reading/writing files, rather than implementing stuff > ourselves. At the very least that would eliminate any inconsistencies between Gromacs and Open Babel generated files. I have implemented GRO format support and OB can read XTC format, so maybe TRR support is the only one really still needed. Problems I have encountered so far with OB is that it spends a lot of time in chain perceiving when the system is solvated, I actually planned to look also if the performance there could be improved. And in general handling of large systems needs improving. Reinis ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
