On 3/16/12 12:36 PM, Alexander Predeus wrote: > Thank you very much for your prompt response! > > I have a small follow-up question. I was under the impression that > refinement is essentially and MD simulation, and thus if I start two > scripts, requesting to generate a 100 models in each, I would end up > with 200 different models. > > I was surprised to see that the scripts actually generate precisely the > same series of models, and with same energies etc. > > Why is that? Is there a way to run several parallel simulations and get > independent sampling, or does it have to go consecutively?

Modeller results are reproducible, so yes, given the same input conditions (including scripts, Modeller version, and operating system) you'll get the same outputs. If you want to get different results, set a different random seed for each of your runs using the rand_seed argument to environ():

http://salilab.org/modeller/9.10/manual/node111.html

Ben Webb, Modeller Caretaker