SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations
Citations
2,418 citations
1,734 citations
1,364 citations
Cites background from "SPFP: Speed without compromise—A mi..."
...It loads a PDB file, models the forces with the AMBER99SB-ILDN force field [20] and TIP-3P water model [21], performs a local energy minimization to eliminate clashes, and then simulates 1 million steps of Verlet dynamics....
[...]
...Since that time, it has found its way into other GPU accelerated MD codes, such as AMBER [36]....
[...]
...All simulations used the AMBER99SB-ILDN force field, a 2 fs time step, rigid water, and constraints on bonds involving hydrogen....
[...]
...We first benchmarked the performance using the AMBER99SB-ILDN force field and TIP3P water model....
[...]
973 citations
771 citations
References
33,683 citations
"SPFP: Speed without compromise—A mi..." refers methods in this paper
...Test systems are droplets and cubic boxes of TIP3Pwater molecules, respectively....
[...]
...An implicit solvent GB simulation of apo-myoglobin (2492 atoms) and an explicit solvent PME simulation of dihydrofolate reductase in a rectangular box of TIP3P [21] water atoms (DHFR, 23,558 atoms including solvent) using the ff99SB [22] version of the AMBER force field were chosen as representative examples of typical research scenarios....
[...]
25,256 citations
"SPFP: Speed without compromise—A mi..." refers methods in this paper
...0 fs were generated with settings as described above for the water droplets, however, using the Berendsen weak coupling thermostat [26] with a target temperature of 300K and a time constant of τT = 10....
[...]
24,332 citations
"SPFP: Speed without compromise—A mi..." refers methods in this paper
...We show that this implementation affords numerical stability that is equivalent to the SPDP precision model, both for generalized Born (GB) [14] implicit solvent simulations, as well as explicit solvent simulations using the particle mesh Ewald (PME) [15] algorithmwhile providing a considerably higher computational throughput, in particular on the newNVIDIA Kepler hardware such as the recently released GTX680 GPU....
[...]
18,394 citations
13,164 citations