Table 5. Deviations of Forces (in kcal/(mol Å)) of the AMBER PMEMD GPU Implementation Using Different Precision Models As Compared to Reference Values Obtained with the CPU Implementation.
| precision model | TRPCage (304 atoms) | ubiquitin (1231 atoms) | apo-myoglobin (2492 atoms) | nucleosome (25 095 atoms) |
|---|---|---|---|---|
| max deviation | ||||
| SPSP | 3.0 × 10–3 | 4.8 × 10–3 | 4.2 × 10–3 | 2.7 × 10–2 |
| SPDP | 5.6 × 10–5 | 3.7 × 10–4 | 1.6 × 10–4 | 1.1 × 10–3 |
| DPDP | 1.1 × 10–8 | 7.3 × 10–8 | 3.4 × 10–8 | 8.0 × 10–8 |
| RMS deviation | ||||
| SPSP | 5.0 × 10–4 | 6.1 × 10–4 | 4.1 × 10–4 | 1.5 × 10–3 |
| SPDP | 7.0 × 10–6 | 1.5 × 10–5 | 8.1 × 10–6 | 3.0 × 10–5 |
| DPDP | 1.5 × 10–9 | 3.6 × 10–9 | 2.6 × 10–9 | 3.2 × 10–9 |