Table 6. Energy Drifts Per Degree of Freedom (kT/ns/dof) from Simulations of 100 ns (TRPCage), 50 ns (Ubiquitin), and 20 ns (Apo-Myoglobin)a.
| time step | 0.5 fs | 1.0 fs | 2.0 fs |
|---|---|---|---|
| TRPCage (304 atoms) | |||
| CPU | 0.000006 | 0.000066 | 0.000355 |
| GPU (DPDP) | 0.000012 | 0.000082 | 0.000382 |
| GPU (SPDP) | 0.000003 | 0.000070 | 0.000222 |
| GPU (SPSP) | 0.000184 | 0.000252 | – |
| ubiquitin (1231 atoms) | |||
| CPU | 0.000004 | 0.000011 | –0.000216 |
| GPU (DPDP) | 0.000001 | 0.000006 | –0.000247 |
| GPU (SPDP) | 0.000003 | 0.000030 | –0.000165 |
| GPU (SPSP) | 0.001065 | 0.000305 | – |
| apo-myoglobin (2492 atoms) | |||
| CPU | 0.000012 | 0.000094 | 0.000416 |
| GPU (DPDP) | –0.000004 | 0.000117 | 0.000290 |
| GPU (SPDP) | 0.000019 | 0.000185 | 0.000139 |
| GPU (SPSP) | 0.002230 | 0.000442* | – |
a
The SHAKE algorithm to constrain bond lengths to hydrogen atoms was used for a time step of 2.0 fs; no constraints were used for smaller time steps. A dash indicates that the system heated up extremely during the simulation to the point that it is meaningless to report an energy drift. An asterisk indicates that the energy drift increases dramatically for longer time scales.