3.5. Comparison of Different Methods GaMD/cMD/aMD¶
The GaMD/aMD methods are closely related and showed very similar performance, as seen in Fig. 3.15. GaMD was slightly less noisy than aMD after reweighting, which was one of its design principles during development.[28] The cMD simulation sampled much less of the conformational space in the same simulation time (see Fig. 3.16). This was expected since no boosting is applied.
Fig. 3.15 dPCA plots of 2000 ns GaMD (left), aMD (middle), and cMD (right) simulations. The middle and right plots are in the same dPCA space as the GaMD simulation.¶
Fig. 3.16 Two shorter cMD simulations (middle and right) compared to the 2000 ns GaMD reference simulation (left). Middle and right are both in the left dPCA space.¶
While the sampling was different between GaMD and cMD, the performance in reproducing experimental NOEs was comparable. The RMSD and other error metrics were similar, indicating that there were no significant differences in reproducing the experimental NOE values.