A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics

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Presentation transcript:

A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics Shweta Purawat, Pek U Ieong, Robert D. Malmstrom, Garrett J. Chan, Alan K. Yeung, Ross C. Walker, Ilkay Altintas, Rommie E. Amaro Biophysical Journal Volume 112, Issue 12, Pages 2469-2474 (June 2017) DOI: 10.1016/j.bpj.2017.04.055 Copyright © 2017 Biophysical Society Terms and Conditions

Figure 1 AMBER GPU MD simulation workflow, showing the uppermost level of the workflow construct. To see this figure in color, go online. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 2 Performance of the AMBER GPU workflow on various systems on a local NVIDIA Tesla K20 cluster. To see this figure in color, go online. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 3 Command line for initiating MD simulations. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 4 Energy minimization plot. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 5 Heating (nonequilibrium) plot. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 6 Time-series analyses (left to right) of the temperature, pressure, and total energy from the third and last stages of equilibration. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 7 Time evolution of the RMSD of (a) copy 1, (b) copy 2, and (c) copy 3 of production MD. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 8 Principal component analysis plot of the p53 simulation result. All the trajectories from the initial run (computer-generated random seed) and the three simulation tests (used the same random seed from the initial run) with 1) Comet (Test 1), 2) private GPU cluster (Test 2), and 3) local machine (Test 3) were first aligned. The first two principal components were then calculated and the trajectories from each test were projected onto the PC space. To see this figure in color, go online. Biophysical Journal 2017 112, 2469-2474DOI: (10.1016/j.bpj.2017.04.055) Copyright © 2017 Biophysical Society Terms and Conditions