Project 9704 (Core 21, GPU, Linux) moving to ADV

[mpharrigan]

Core 21 is the next generation of OpenMM-based GPU cores. It uses OpenMM 6.2.

This project studies the same system as p9752:

Sodium channels initiate signaling in neurons and other cells which go on to become sensations of pleasure and pain, as well as thoughts and feelings. Sodium channel malfunction has been linked with cardiac arrhythmia, epilepsy, and neuropathic pain. These projects simulate a whole voltage-gated sodium channel in a bi-lipid membrane based on crystal structures deduced only recently (2013). The channel is made up of four homologous domain which form a pore through the membrane. The "top" (extracellular) end of the pore selects for sodium ions only. The "bottom" (intracellular) region can be open or closed. Each pore domain is linked to a voltage-sensing domain, which causes the channel to open or close based on the electrical environment of the membrane. We aim to study the dynamics of transitions between the open and closed states mediated by the voltage sensing domains. Our experimental collaborators will probe sodium channel function through the use of natural toxins secreted by frogs in the Amazon rainforest. By combining theory and experiment, we can propose and test derivatives of these toxins which have positive therapeutic effects.

Runs: 245
Clones: 20
Gens: 781
Base credit: 9000
Timeout: 1 day
Deadline: 5 days
Number of atoms: ~175k
OS: Linux only (for now)

This project is constrained to run on systems with CPU RAM > 2000 MiB. While most compute happens on the GPU, general bookkeeping is managed by the CPU and CPU RAM. This large project uses a noteworthy amount of CPU RAM. There is no constraint on amount of GPU RAM. The GPU RAM used by this project is in line with most FAH GPU projects.

This project is Linux only for now. 32-bit Windows can only address 2 GB of (CPU) RAM. We're actively working on a 64-bit windows version of core 21, which will be able to run this project.

Happy folding!