SireAdvanced Molecular Simulation Framework

I've time to blog while I am waiting for the Python wrappers to compile (they are pretty much all recompiling from scratch, so it will be a while!). Over the last few days I've been writing an 'Ensemble' class that allows me to describe the ensemble sampled by a move, or a group of moves. This became necessary as it was getting difficult to ensure that the right replica exchange test was being used for the different combinations of moves of the different replicas.

I got a new book today - C++ Template Metaprogramming: Concepts, Tools, and Techniques from Boost and Beyond.

Well, I hope you approve of the new website. It took most of Sunday, but I eventually got everything installed and updated. I've decided to start adding some actual content to the site (rather than just using it as a fancy blog). To that end, I've started writing an introduction to C++, which is the in the introduction to the design of Sire (see the software design link on the left). This will give enough background in C++ that I can then start describing the design of Sire. This will provide a higher level of documentation than is currently available (at the moment, Sire is documented purely at the source code level, via doxygen comments).

I am in the process of updating the Sire website - both to update to the latest version of drupal (the content managment software used for this site - I was on version 5, but have upgraded to version 6.5) - and to being the process of making this site a little more professional.

Long time no blog!

I am now *so* close to having Sire working again. I've spent the last few months with quite broken code because I reworked the SireMol library (which provides all of the data structures that actually define a molecule). Well, SireMol is now nearly finished, and the update is definitely worth it! As I've blogged before, the updated data structure allows pretty much any piece of data in a molecule to be attached as a property. This includes such basic concepts as the element types of the atoms, their coordinates and their identifications.

2008 already! There's only been a couple of weeks of 2008 so far, but I feel like I've already managed to get a lot done. The multiscale review chapter is now finished and with our editor, so we met the deadline and it will appear in this year's Royal Society of Chemistry special periodical review. Biased as I am, I think that it is quite a nice review. It covers developments from 2005-2007 in biomolecular simulation from quantum methods up to continuum methods, in particular methods that involve the combination of at least two different levels of modelling (e.g.

Happy Christmas everyone! The holidays are now here, so it's time to take a break from the keyboard and relax for a bit.

There's been a small delay with publication - we only received the proofs this weekend, so unfortunately the paper didn't make it into a November JCP. Hopefully it should make it into a December JCP so that it is published in 2007. Speaking of papers, I am currently finishing off a review of multiscale modelling of biomolecular systems. There's been a lot of really clever ideas and progress over the last 2-3 years in this field, and it is now possible to perform some really cool simulations that capture a very wide range of length and time scales.

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.