I don't think we have ever tried nearly that many restraints, so there may be some inefficiency that we haven't noticed. One possibility is building the dependency graph which is used to figure out the relationship between restraints and particles and scores states. Another is the non-bonded list or lists if you have many packed particles. It can be a bit difficult to control memory usage and in fact there was a bug a bit back with their memory usage increasing uncontrollably. For tracking down problems, if you have a mac where you can run things, there is a wonderful program there called "Instruments" which can track all memory allocations and deallocations and report where they were done. I would also suggest first updating to a more recent version of IMP to see if it is the non-bonded bug. On Jun 7, 2011, at 7:52 AM, Davide Baù wrote:
|