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. Author manuscript; available in PMC: 2018 Nov 14.
Published in final edited form as: J Chem Theory Comput. 2017 Oct 19;13(11):5753–5765. doi: 10.1021/acs.jctc.7b00840

Table 4.

CPU time spent for 10 ps of MD simulation (5,000 steps with 2 fs time step for AA/exp, AA/GBMV, and AA/CG models and 2,500 steps with 4 fs time step for CG model) for five different protein systems. AA/exp refers to simulations with explicit water or water and POPC lipids (bacteriorhodopsin). All the simulations were performed in serial on a single core of an Intel E5–2680v3 processor (2.5 GHz) using CHARMM c41a1. CPU times are provided in seconds. Speedups with respect to AA/GBMV are provided in parentheses.

System AA/exp. AA/GBMV AA/CG CG
Trp-cage 802 216 150 (1.4) 21 (10.3)
SH3 1139 820 584 (1.4) 80 (10.3)
Protein G 1689 715 316 (2.3) 74 (9.7)
Bacteriorhodopsin 3090 3219 1786 (1.8) 307 (10.5)
Adenylate kinase 3101 2915 1374 (2.1) 293 (9.9)