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   benchmark results

Tinker


13. Benchmark Results

The tables in this section provide CPU benchmarks for basic TINKER energy evaluations. All times are in seconds and were measured with TINKER 3.8, dimensioned to MAXATM of 10000 and MAXHESS of 1000000. Each benchmark was run twice in rapid succession on a quiet machine. Times reported are the fastest results from the second run. If you are able to run the benchmarks on additional machine types, please send the results for inclusion in a future listing.

BENCHMARK #1: Calmodulin Energy Evaluation

The system is an isolated molecule of the 148-residue protein calmodulin with 2264 atoms using the Amber-94 force field. All interactions are computed with no use of cutoffs. Times listed are for calculation setup followed by a single energy, energy/gradient and Hessian evaluation.
MACHINE TYPE MHz SETUP ENERGY GRAD HESS
Compaq DS10 (Tru64 5.0) 466 0.22 1.27 2.01 7.47
DEC Alpha 4100 (Tru64 5.0) 400 0.37 3.20 4.92 17.28
DEC Alpha 200 4/233 (Tru64 5.0) 233 1.22 6.92 11.81 55.17
SGI IndigoII R10K (Irix 6.5) 195 0.86 3.61 5.98 22.93
SGI IndigoII R4400 (Irix 6.5) 200 1.96 8.10 16.24 63.52
Target-USA Athlon (RH 6.2, PGI) 950 0.27 0.77 1.63 7.32
Target-USA Athlon (RH 6.2, Absoft) 950 0.25 0.96 1.73 8.56
Target-USA Athlon (RH 6.2, g77) 950 0.30 0.81 1.57 9.91
Target-USA Athlon (RH 6.2, f2c,gcc) 950 0.29 0.76 1.87 9.79
Compaq Armada M700 (RH 6.2, PGI) 650 0.29 1.37 3.25 13.57
Compaq Armada M700 (RH 6.2, Absoft) 650 0.27 1.57 3.31 15.53
Compaq Armada M700 (RH 6.2, g77) 650 0.30 1.75 3.44 17.94
Compaq Armada M700 (RH 6.2, f2c,gcc) 650 0.30 1.62 3.87 16.55
Compaq Armada M700 (Win2K, CVF 6.5) 650 0.25 1.25 2.85 12.13 

BENCHMARK #2: Crambin Crystal Energy Evaluation

The system is a unit cell of the 46-residue protein crambin containing 2 polypeptide chains, 2 ethanol and 178 water molecules for a total of 1360 atoms using the OPLS-UA force field. Periodic boundaries are used with particle mesh Ewald for electrostatics and a 9.0 Å cutoff for vdW interactions. Times listed are for calculation setup followed by a single energy, energy/ gradient and Hessian evaluation.
MACHINE TYPE MHz SETUP ENERGY GRAD HESS 
Compaq DS10 (Tru64 5.0) 466 0.21 0.49 0.65 1.92
DEC Alpha 4100 (Tru64 5.0) 400 0.35 0.81 1.04 3.15
DEC Alpha 200 4/233 (Tru64 5.0) 233 1.13 2.36 3.26 9.52
SGI IndigoII R10K (Irix 6.5) 195 0.78 0.94 1.42 3.96
SGI IndigoII R4400 (Irix 6.5) 200 1.81 2.81 4.29 12.96
Target-USA Athlon (RH 6.2, PGI) 950 0.27 0.32 0.47 1.34 
Target-USA Athlon (RH 6.2, Absoft) 950 0.22 0.37 0.53 1.58
Target-USA Athlon (RH 6.2, g77) 950 0.27 0.41 0.58 1.77
Target-USA Athlon (RH 6.2, f2c,gcc) 950 0.29 0.45 0.69 1.75
Compaq Armada M700 (RH 6.2, PGI) 650 0.28 0.51 0.75 2.45
Compaq Armada M700 (RH 6.2, Absoft) 650 0.22 0.64 0.89 3.19
Compaq Armada M700 (RH 6.2, g77) 650 0.31 0.70 0.98 3.27
Compaq Armada M700 (RH 6.2, f2c,gcc) 650 0.29 0.71 1.06 3.26
Compaq Armada M700 (Win2K, CVF 6.5) 650 0.23 0.50 0.69 2.32 

BENCHMARK #3: Peptide Normal Mode Calculation

The system is a minimum energy conformation of a 20-residue peptide containing one of each of the standard amino acids for a total of 328 atoms using the OPLS-AA force field without cutoffs. The time reported is for computation of the Hessian and calculation of the normal modes of the Hessian matrix and the vibration frequencies requiring two separate matrix diagonalization steps.
MACHINE TYPE MHz NORMAL MODES

Compaq DS10 (Tru64 5.0) 466 41
DEC Alpha 4100 (Tru64 5.0) 400 90
DEC Alpha 200 4/233 (Tru64 5.0) 233 343
SGI IndigoII R10K (Irix 6.5) 195 145
SGI IndigoII R4400 (Irix 6.5) 200 362
Target-USA Athlon (RH 6.2, PGI) 950 51
Target-USA Athlon (RH 6.2, Absoft) 950 54
Target-USA Athlon (RH 6.2, g77) 950 63
Target-USA Athlon (RH 6.2, f2c,gcc) 950 84
Compaq Armada M700 (RH 6.2, PGI) 650 64
Compaq Armada M700 (RH 6.2, Absoft) 650 69
Compaq Armada M700 (RH 6.2, g77) 650 117
Compaq Armada M700 (RH 6.2, f2c,gcc) 650 119
Compaq Armada M700 (Win2K, CVF 6.5) 650 63 

BENCHMARK #4: TIP3P Water Box Molecular Dynamics

The system consists of 216 rigid TIP3P water molecules in a 18.643 Å periodic box, 9.0 Å shifted energy switch cutoffs for nonbonded interactions. The time reported is for 1000 dynamics steps of 1.0 fs each using the modified Beeman integrator and Rattle constraints.
MACHINE TYPE MHz DYNAMICS
Compaq DS10 (Tru64 5.0) 466 99
DEC Alpha 4100 (Tru64 5.0) 400 221
DEC Alpha 200 4/233 (Tru64 5.0) 233 577
SGI IndigoII R10K (Irix 6.5) 195 263
SGI IndigoII R4400 (Irix 6.5) 200 866
Target-USA Athlon (RH 6.2, PGI) 950 70
Target-USA Athlon (RH 6.2, Absoft) 950 78 
Target-USA Athlon (RH 6.2, g77) 950 86
Target-USA Athlon (RH 6.2, f2c,gcc) 950 93
Compaq Armada M700 (RH 6.2, PGI) 650 130
Compaq Armada M700 (RH 6.2, Absoft) 650 142
Compaq Armada M700 (RH 6.2, g77) 650 155
Compaq Armada M700 (RH 6.2, f2c,gcc) 650 169
Compaq Armada M700 (Win2K, CVF 6.5) 650 130 

BENCHMARK #5: TINKER Water Box Molecular Dynamics

The system consists of 216 TINKER flexible polarizable atomic multipole water molecules in a 18.643 Å periodic box using regular Ewald summation for the electrostatics and a 12.0 Å switched cutoff for vdW interactions. The time reported is for 100 dynamics steps of 1.0 fs each using the modified Beeman integrator and 0.01 Debye rms convergence for induced dipole moments.
MACHINE TYPE MHz DYNAMICS
Compaq DS10 (Tru64 5.0) 466 288
DEC Alpha 4100 (Tru64 5.0) 400 515
DEC Alpha 200 4/233 (Tru64 5.0) 233 2016
SGI IndigoII R10K (Irix 6.5) 195 816
SGI IndigoII R4400 (Irix 6.5) 200 3048
Target-USA Athlon (RH 6.2, PGI) 950 287
Target-USA Athlon (RH 6.2, Absoft) 950 316
Target-USA Athlon (RH 6.2, g77) 950 365
Target-USA Athlon (RH 6.2, f2c,gcc) 950 370
Compaq Armada M700 (RH 6.2, PGI) 650 490
Compaq Armada M700 (RH 6.2, Absoft) 650 520
Compaq Armada M700 (RH 6.2, g77) 650 606
Compaq Armada M700 (RH 6.2, f2c,gcc) 650 603
Compaq Armada M700 (RH 6.2, CVF 6.5) 650 446



© Goodman Group, 2005-2017; privacy; last updated November 16, 2017

department of chemistry University of Cambridge