Benchmarks: Difference between revisions
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* '''basic:''' Structure calculation of a protein with 114 amino acid residues, 1737 NOE distance restraints, 110 torsion angle restraints. 50 conformers are calculated using 4000 torsion angle dynamics steps per conformer. | * '''basic:''' Structure calculation of a protein with 114 amino acid residues, 1737 NOE distance restraints, 110 torsion angle restraints. 50 conformers are calculated using 4000 torsion angle dynamics steps per conformer. | ||
* '''auto:''' Structure calculation with automated NOESY assignment of a protein with 114 amino acid residues, | * '''auto:''' Structure calculation with automated NOESY assignment of a protein with 114 amino acid residues, 4732 NOESY cross peaks, 88 torsion angle restraints. 8 x 100 = 800 conformers are calculated using 10000 torsion angle dynamics steps per conformer. | ||
* '''test suite:''' Complete CYANA 3.0 test suite, comprising the 'basic' and 'auto' calculations, as well as structure calculations for homodimers, using RDCs, pseudocontact shifts, etc. | * '''test suite:''' Complete CYANA 3.0 test suite, comprising the 'basic' and 'auto' calculations, as well as structure calculations for homodimers, using RDCs, pseudocontact shifts, etc. | ||
Revision as of 20:25, 3 December 2008
Benchmark types:
- basic: Structure calculation of a protein with 114 amino acid residues, 1737 NOE distance restraints, 110 torsion angle restraints. 50 conformers are calculated using 4000 torsion angle dynamics steps per conformer.
- auto: Structure calculation with automated NOESY assignment of a protein with 114 amino acid residues, 4732 NOESY cross peaks, 88 torsion angle restraints. 8 x 100 = 800 conformers are calculated using 10000 torsion angle dynamics steps per conformer.
- test suite: Complete CYANA 3.0 test suite, comprising the 'basic' and 'auto' calculations, as well as structure calculations for homodimers, using RDCs, pseudocontact shifts, etc.
Computer systems:
- Desktop: Desktop computer with 1 Intel Core2 Quad CPU Q6600, 2.40 Ghz, 3.0 GB memory, Ubuntu 8.04 Linux, gfortran (-O3) Fortran compiler.
- Server: Linux cluster system with 20 nodes, each having 2 Intel Xeon Quad CPU E5462, 2.80 Ghz, 16 GB memory, Ubuntu 8.04 Linux, gfortran (-O3) Fortran compiler.
Benchmark results:
| System | processors | basic | auto | test suite |
| Desktop | 1 | x | x | x |
| Desktop | 4 | ? | ? | ? |
| Server | 1 | 144 | ? | ? |
| Server | 10 | 16 | 762 | 2997 |
| Server | 20 | 10 | 420 | 1623 |
| Server | 100 | 5 | 152 | 529 |