I'm a postdoc in the Pande group. This is my first series of projects on FAH
Here is the description:===
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: (1) run computations for the insulin monomer and the insulin dimer; (2) use the model of the insulin monomer from step 1 and our new method to build a model of the insulin dimer; (3) compare the model of the dimer built by our new method (from step 2) with the model of the dimer obtained directly from the simulations for the dimer (from step 1), and see whether our new method works.
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Projects 9810-9817, which I'm now releasing to Advanced, are about insulin monomer under physiological conditions. Projects for a monomer under the conditions that were used by our collaborators - experimentalists, as well as projects for insulin dimer, are under preparation. In 9810-9817, I have 81 runs with different number of atoms in the box (10K to 18K), and I grouped them into 8 projects with approximately the same number of atoms: project 9810 for 10K atoms, 9811 for 11K atoms, etc. Credits are also slightly different (benchmarked against comparable projects currently running on FAH):
project natoms, 10^3 base credit
9810 10000 11461
9811 11000 11745
9812 12000 13403
9813 13000 15548
9814 14000 17078
9815 15000 18358
9816 16000 18433
9817 18000 19054
Deadline 14.0 days, timeout 10.0 days, k-factor 0.75.
All GPU types (hopefully), Linux/Win
Thank you!