SireAdvanced Molecular Simulation Framework

Sire is now being used for full production simulations by several users. Again, the transition from a development code to a production code took me by surprise, but once it started working, then it was working very well. So far I have five users (including an installation at another university) and they are running a range of different simulations. What has been interesting is the ease by which they are able to modify the code to get it to do what they want. I provided them with a base python script that sort of did what they wanted, and then they adapted those scripts to refine the simulation (the most impressive was one student who took a script that calculated the relative free energy between an MM and QM model, and use it to calculate relative free energies between different QM models - yes - we now know the free energy difference of including electron correlation by going from HF to MP2, or from MP2 to CCSD(T), or of increasing the size of the basis set!). Other modifications have included taking a script that performed Monte Carlo using a rigid solvent and changing it to use a flexible solvent (so we have a fully flexible box of n-methyl-acetamide - something that ProtoMS could never do, as it was limited to rigid solvents). I am currently using Sire to run some absolutely massive simulations - calculating the relative binding free energies of neuraminidase ligands using a DFT/BLYP/VDZ model of the ligands (running multiple lambda values between the QM and MM models, and up to 10M MC moves per lambda value). I am using 48 processor cores per simulation, and have about 1000 cores running on the Bristol supercomputer (aren't I lucky!). I am now busy running around trying to manage everything and everyone as we are now processing results for publication.