Table 2.
The performance times of the different methods under study. a
| PDLD/S-LRA/β | LRA/β | LIE | PDLD/S-LRA/β (fast version) | |
|---|---|---|---|---|
| Water sampling (MD) | - | 40ps (56.56 min) | 20ps (28.28 min) | - |
| Protein sampling (MD) | 40ps (76.42 min) | 40ps (76.42 min) | 20ps (38.21 min) | 4ps (7.64 min) |
| PDLD/S calculations | 12.2 min | - | - | 1.22 min |
a
The results reported here are for a protein of ~170 amino acid residues. We prepare the system with a 40ps relaxation run (takes ~108.4 min). The calculations were conducted on the University of Southern California HPCC (High Performance Computing and Communication) Linux computer, using the Dual Intel P4 3.0 GHz 2GB Memory nodes.