moving p9842 to ADVANCED

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moving p9842 to ADVANCED

Postby sinitskiy » Mon Dec 04, 2017 3:41 pm

Hi all,

I'm moving project p9842 to ADVANCED. It is very similar to 9839-9841. I only took several most interesting geometries generated in p9841 so far, and now starting more simulations from these interesting geometries.

base credit 3068
28K atoms
Deadline 5 days, timeout 4 days, k-factor 0.75.
NVidia/ATI GPUs, only Linux, GPUSpecies<7 (for newer GPUs we had issues with too low PPDs)

The science is the same as earlier in projects 9810-9817 and 9820-9827, but now it's an insulin dimer, while those were monomers:

Go big by going… small! We want to study really large proteins and protein complexes, maybe as large as ribosomes or ion channels in neurons. One possible way to reach this goal is to run computations for each part of a big complex separately, and then assemble the resulting models together. We think we know how to do so, but first we need to test our approach on simpler systems.

Insulin is a small protein used by the pancreas to signal to the whole organism whether to consume more glucose or not. Disruptions in the processes of secreting and sensing insulin lead to various diseases, including diabetes mellitus, metabolic syndrome and polycystic ovary syndrome. Insulin can form dimers (complexes consisting of two insulin molecules), hexamers (complexes of six insulin molecules) and even larger aggregates resembling those formed under Alzheimer’s, but only the monomer is physiologically active. In this project, we want to run simulations of insulin monomers and dimers and see whether our methodology for studying big systems works here.


Looking forward to your feedback!
Thanks a lot
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