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Table 1 Experiment 1 executes the 7 stages of the ESMACS protocol with a null workload; Experiment 2 uses the actual MD workload of the ESMACS protocol

From: High-throughput binding affinity calculations at extreme scales

Experiment ID

Protocol

Workload

# Trials

# Pipelines

# Stages

# Tasks

# Cores per pilot

1

ESMACS

Null workload

2

8, 16, 32, 64, 128

7

7

64, 128, 256, 512, 1024

2

ESMACS

EGFR kinase Workload

2

8, 16, 32, 64, 128

7

7

64, 128, 256, 512, 1024

  1. ESMACS protocol with EGFR kinase workload: (1) Untar configuration files; (2) Preprep; (3) Minimize with decreasing restraints; (4) Equilibration: NVT simulation at 50K, with restraints; (5) Equilibration: NPT simulation at 300K, with decreasing restraints; (6) Equilibration: NPT at 300k, no constraints; (7) Tarball output files
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BMC Bioinformatics

ISSN: 1471-2105

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