Hmm.. It may actually still have been caclulating the MD deformations. MD is very resource intensive and can take an absolute age to perform its calcs. I have heard that acceptable results can be achieved by getting MD to calculate the motion with a low poly stand in (then you simply save and re-import the MDD files with your production scene), but this potentially could lead to some deformation errors.
My best suggestion would be to (a) make sure you only have enough polys for what you need, and (b) before killing the simulation, check Windows Task manager to ensure that the application process isn't sitting totally at zero CPU time...
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