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pcbi.1008308.g003.tif (220.75 kB)

Benchmark results for AWSEM-3SPN2 simulations of protein-DNA complexes using the LAMMPS and the OpenMM implementations of both forcefields on a linear scale (left) and on a log scale (right).

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posted on 2021-02-12, 18:41 authored by Wei Lu, Carlos Bueno, Nicholas P. Schafer, Joshua Moller, Shikai Jin, Xun Chen, Mingchen Chen, Xinyu Gu, Aram Davtyan, Juan J. de Pablo, Peter G. Wolynes

The x-axis shows the PDB ID. The y-axis shows the computer hours needed to simulate for 1 million steps. Each complex was simulated 5 times using each implementation. The protein length ranges from 52 nucleotides to 2050 amino acids, while the DNA length ranges from 2 to 40 nucleotides.