The project estrogen_namd has been activated with the POC being Gyorgy Babnigg. They have been granted 45k till the end of the year. - JB On Mon, Apr 13, 2015 at 4:20 PM, Bair, Raymond A. <[email protected]> wrote:
This 45K project will use biggpu nodes.
The class, subclass and POC would be the same as project Drude. Prio 3.
Looks OK to approve.
Ray
On 4/13/15, 11:48 AM, "[email protected]" <[email protected]> wrote:
Hello,
A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee.
Applicant's name: wei jiang Applicant's institution: ANL Applicant's division: Leadership Computing Facility Project Name: estrogen_namd Project title: Long-scale conformational activation in estrogen receptor with NAMD on GPU/CPU heterogeneous architecture Associated funding: ALCF fund DOD grant Other Systems: Mira Science: Structure-function relation of protein; Developing SIMD version force kernel for namd; Compare simd version CPU and GPU/CPU performance. Project description: Wei Jiang, Sunhwan Jo, Sichun Yang
Leadership Computing Facility, Argonne National Laboratory Case Western Reserve University, Department of Pharmacology
The ligand-binding domain (LBD) of an estrogen receptor undergoes a large conformational switching from an inactive to active state in response to hormone stimuli (see figure below). Very recently, a novel D538G mutant has been identified to be active in advanced breast cancer tumors. Despite being the key target for breast cancer therapeutics, the LBD is a remarkable example of conformational switching, where the dynamics of a C-terminal α-helix H12 from an inactive to active conformation remains unclear. The inactive conformation can be stabilized by therapeutic inhibitors such as tamoxifen, so H12 is in a helix-bundle forming conformation (marked in blue in Figure) that can block the receptor from recruiting coactivators for transcriptional activation. Once activated by estrogen binding, H12 is switched to a completely different orientation covering the estrogen-binding pocket in the active conformation (marked in red). These two well-defined conformations—active and inactive—have been revealed extensively by crystallographic studies. Our recent coarse-grained molecular dynamics shows such a transition could take at least in the order of 100 ns (Huang et al, JCTC, 10 (8) 2897–2900, 2014). While this information is highly informative, a key question remains, i.e., whether the mutation affects the active state only or sculpts the entire landscape, including both inactive and active states. To answer this question from a broad landscape perspective, the modeling of such a large-scale H12 transition can be quite challenging for atomic-level simulations using the standard CPU-based MD simulations. To obtain long-scale and long-time MD trajectories, we propose to use the GPU version (Nvidia CUDA) NAMD package on the Blues bigmem GPU/CPU nodes. NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. In this proposal, in addition to the brutal-force GPU/CPU work, we also explore AVX256 instruction set to optimize force kernel of NAMD for state-of-th e-art Intel architecture. A fully vectorized force kernel with AVX256 also provides a better reasonable CPU performance reference for GPU. In this proposal we apply a total 45,000 cpu hours, including both long production run on GPU/CPU nodes and code development with AVX256.
Industry partnership: Project URL: Requested allocation: 45000 Q1: 0 Q2: 0 Q3: 20000 Q4: 25000 Justification: NAMD is the only one MD code that can run at strong scaling on massively distributed GPU/CPU platform such as Cray XT7. Storage requirements: 1 TB
The requester has used undetermined amount hours of their initial startup project.
In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see:
https://wiki.lcrc.anl.gov/wiki/Processes/Categories
Once the Allocation committee has approved the project, please go to the Project Management page to create it:
https://accounts.lcrc.anl.gov/projects.php
Thank You, The LCRC Accounts System
_______________________________________________ allocations-admins mailing list [email protected] https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins