Published!
Scientific results generated using Sire have now been accepted for publication in the Journal of Chemical Physics (we've been told that the paper should be in issue 28 published in November). This is a major milestone for Sire, and hopefully the first of many papers published using this code. Also, and perhaps surprisingly, this is the first paper that I've had accepted that has results that were generated using ProtoMS, my other molecular simulation code. While ProtoMS has been used in other papers (the first was Caterina's paper on calculating absolute binding free energies of tightly bound waters), I had not personally used ProtoMS in anger before to produce published results (I only used an early version to produce the protein/ligand free energies in my thesis, and as the system was p38 kinase, none of the free energies were anywhere near experiment, and so we didn't bother publishing them - as an aside - p38 kinase, like most kinases, presents major difficulties for binding free energy simulations, and I will know that I have finally created a proper, fully working and predictive free energy method when I can finally calculate accurate free energies for p38!). I've tagged the version of Sire used to produce the results in the paper, so if you want, you can download it by typing;
svn co http://sire.googlecode.com/svn/tags/jchemphys07_paper
I'll place the input files necessary to run the published experiments up on this website some time this week (assuming I can get permission), and I'll also try to put up the extra code that is needed to link Molpro to Sire (Molpro was used to perform the QM energy calculations).
Progress on Sire is going well. I've now almost finished the complete rewrite of the molecule representation. Molecules can now hold pretty much any data, in any format, which makes it now very straightforward to have multiple representations of a molecule held within a single container (and to save and restore these representations to a file, or send them over a network). This will come in very handy if I am successful with my fellowship applications, as I am proposing to run some large multiscale simulations using Sire that will involve modelling molecules using both an atomistic and coarse grain representation simultaneously. While Sire has been designed from the start to handle this type of simulation, the rewrite now makes it very easy to setup and control the multiple representations, and should as well provide a nice interface for it all. Of course now that I've rewritten SireMol, I've now got to propogate out the update across all of the other modules... In most cases this will be easy, as object orientated design hides the implementation - however the rewrite allows me to write much simpler code, as the interfaces are now more powerful, so there are quite a few things that will need to be updated.
