Fig. 2: Evaluation of energy and force calculations by AI2BMD and MM.
From: Ab initio characterization of protein molecular dynamics with AI2BMD
a, Folded structures of nine evaluated proteins. For these proteins, the number of atoms ranges from 175 to 13,728. b–e, The MAE of potential energy (b,c) and atomic force (d,e). For each protein, we conducted replica-exchange MD and structure clustering to select representative structures, including folded, unfolded or intermediate states. AI2BMD simulations were conducted for the representative structures, and 200 samples in total were selected for evaluation. For the first 5 proteins within 1,040 atoms shown in b,d, DFT calculation for the whole protein performed by ORCA with the same settings in dataset generation is set as the reference value, whereas for the last 4 proteins shown in c,e, the reference value is set as the fragment DFT calculation owing to prohibitive computational cost. In b,c, the potential energy of each structure has that of the initial folded structure subtracted, and then is normalized by the number of atoms. The error bars in b–e indicate the standard deviations of the potential energy and atomic force of 200 different samples of the protein (n = 200), with each sample shown as a filled circle. f, Comparison of time consumption of energy calculation for nine proteins. DFT calculations were carried out on a GPU. For the last five proteins, the time consumption by DFT was estimated by the fitting curve from those of the first four proteins and is shown with a dashed line and circles. The inset shows a comparison for the first four proteins.
