# Benchmark Results

The tables in this section provide CPU benchmarks for basic Tinker energy and derivative evaluations, vibrational analysis and molecular dynamics. All times are in seconds and were measured with Tinker executables dimensioned to maxatm of 10000 and maxhess of 1000000 in the source file sizes.i. All calculations were run twice in rapid succession on a quiet machine. The times reported for each benchmark are the results from the second run. If you have built Tinker on an alternative machine type and are able to run the benchmarks on the additional machine type, 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 ff94 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-OS-COMPILER TYPE MHz SETUP ENERGY GRAD HESS

> Athlon XP 2400+ (RH 8.0, Intel) 2000 0.13 0.28 0.60 2.96 Athlon XP 2400+ (RH 8.0, PGI) 2000 0.16 0.31 0.70 3.60 Athlon XP 2400+ (RH 8.0, g77 3.2) 2000 0.17 0.28 0.66 3.67 Athlon Thunderbird (RH 8.0, Intel) 1400 0.22 0.41 0.86 5.15 Athlon Thunderbird (RH 8.0, PGI) 1400 0.21 0.44 1.00 5.92 Athlon Thunderbird (RH 8.0, g77 3.2) 1400 0.19 0.40 0.94 5.81 Athlon Classic (RH 8.0, Intel) 950 0.30 0.64 1.42 7.07 Athlon Classic (RH 8.0, PGI) 950 0.30 0.69 1.65 7.96 Athlon Classic (RH 8.0, g77 3.2) 950 0.31 0.63 1.57 7.94 Compaq Evo N610c P4 (RH 8.0, Intel) 2000 0.18 0.45 0.87 3.08 Compaq Evo N610c P4 (RH 8.0, PGI) 2000 0.22 0.44 1.06 4.27 Compaq Evo N610c P4 (RH 8.0, Absoft) 2000 0.17 0.52 1.06 3.95 Compaq Evo N610c P4 (RH 8.0, g77 3.2) 2000 0.19 0.41 1.07 4.41 Compaq Evo N610c P4 (WinXP, CVF 6.6) 2000 0.16 0.38 0.98 3.54 Compaq Evo N610c P4 (WinXP, g77 3.2) 2000 0.16 0.40 1.08 4.45 Apple Power Mac G4 (OSX 10.2, Absoft) 733 0.41 2.96 5.12 17.83 Apple Power Mac G4 (OSX 10.2, g77 3.3) 733 0.37 1.98 3.79 14.48 Compaq AlphaServer DS10 (Tru64 5.0) 466 0.35 1.33 1.93 8.40 SGI IndigoII R10K (Irix 6.5, MIPS) 195 1.17 3.49 6.35 23.03

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 Angstrom cutoff for vdW interactions. Times listed are for calculation setup followed by a single energy, energy/ gradient and Hessian evaluation.

MACHINE-OS-COMPILER TYPE MHz SETUP ENERGY GRAD HESS

> Athlon XP 2400+ (RH 8.0, Intel) 2000 0.12 0.12 0.21 0.66 Athlon XP 2400+ (RH 8.0, PGI) 2000 0.13 0.14 0.24 0.63 Athlon XP 2400+ (RH 8.0, g77 3.2) 2000 0.14 0.13 0.28 0.81 Athlon Thunderbird (RH 8.0, Intel) 1400 0.19 0.17 0.30 0.91 Athlon Thunderbird (RH 8.0, PGI) 1400 0.18 0.18 0.32 0.91 Athlon Thunderbird (RH 8.0, g77 3.2) 1400 0.17 0.17 0.38 1.11 Athlon Classic (RH 8.0, Intel) 950 0.26 0.25 0.47 1.46 Athlon Classic (RH 8.0, PGI) 950 0.29 0.27 0.50 1.42 Athlon Classic (RH 8.0, g77 3.2) 950 0.27 0.27 0.56 1.70 Compaq Evo N610c P4 (RH 8.0, Intel) 2000 0.15 0.14 0.27 0.64 Compaq Evo N610c P4 (RH 8.0, PGI) 2000 0.22 0.19 0.33 0.88 Compaq Evo N610c P4 (RH 8.0, Absoft) 2000 0.14 0.22 0.39 0.84 Compaq Evo N610c P4 (RH 8.0, g77 3.2) 2000 0.15 0.20 0.45 1.13 Compaq Evo N610c P4 (WinXP, CVF 6.6) 2000 0.14 0.17 0.33 0.83 Compaq Evo N610c P4 (WinXP, g77 3.2) 2000 0.12 0.22 0.52 1.16 Apple Power Mac G4 (OSX 10.2, Absoft) 733 0.32 0.58 1.09 3.11 Apple Power Mac G4 (OSX 10.2, g77 3.3) 733 0.31 0.42 0.79 2.37 Compaq AlphaServer DS10 (Tru64 5.0) 466 0.29 0.38 0.64 1.95 SGI IndigoII R10K (Irix 6.5, MIPS) 195 0.92 0.74 1.41 3.89

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-OS-COMPILER TYPE MHz NORMAL MODES

> Athlon XP 2400+ (RH 8.0, Intel) 2000 22 Athlon XP 2400+ (RH 8.0, PGI) 2000 26 Athlon XP 2400+ (RH 8.0, g77 3.2) 2000 24 Athlon Thunderbird (RH 8.0, Intel) 1400 31 Athlon Thunderbird (RH 8.0, PGI) 1400 34 Athlon Thunderbird (RH 8.0, g77 3.2) 1400 33 Athlon Classic (RH 8.0, Intel) 950 46 Athlon Classic (RH 8.0, PGI) 950 51 Athlon Classic (RH 8.0, g77 3.2) 950 48 Compaq Evo N610c P4 (RH 8.0, Intel) 2000 19 Compaq Evo N610c P4 (RH 8.0, PGI) 2000 19 Compaq Evo N610c P4 (RH 8.0, Absoft) 2000 20 Compaq Evo N610c P4 (RH 8.0, g77 3.2) 2000 19 Compaq Evo N610c P4 (WinXP, CVF 6.6) 2000 19 Compaq Evo N610c P4 (WinXP, g77 3.2) 2000 20 Apple Power Mac G4 (OSX 10.2, Absoft) 733 67 Apple Power Mac G4 (OSX 10.2, g77 3.3) 733 62 Compaq AlphaServer DS10 (Tru64 5.0) 466 39 SGI IndigoII R10K (Irix 6.5, MIPS) 195 144

BENCHMARK #4: TIP3P Water Box Molecular Dynamics

The system consists of 216 rigid TIP3P water molecules in a 18.643 Angstrom periodic box, 9.0 Angstrom 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 on all bond lengths.

MACHINE-OS-COMPILER TYPE MHz DYNAMICS

> Athlon XP 2400+ (RH 8.0, Intel) 2000 37 Athlon XP 2400+ (RH 8.0, PGI) 2000 34 Athlon XP 2400+ (RH 8.0, g77 3.2) 2000 45 Athlon Thunderbird (RH 8.0, Intel) 1400 52 Athlon Thunderbird (RH 8.0, PGI) 1400 47 Athlon Thunderbird (RH 8.0, g77 3.2) 1400 63 Athlon Classic (RH 8.0, Intel) 950 77 Athlon Classic (RH 8.0, PGI) 950 71 Athlon Classic (RH 8.0, g77 3.2) 950 96 Compaq Evo N610c P4 (RH 8.0, Intel) 2000 53 Compaq Evo N610c P4 (RH 8.0, PGI) 2000 54 Compaq Evo N610c P4 (RH 8.0, Absoft) 2000 55 Compaq Evo N610c P4 (RH 8.0, g77 3.2) 2000 91 Compaq Evo N610c P4 (WinXP, CVF 6.6) 2000 63 Compaq Evo N610c P4 (WinXP, g77 3.2) 2000 94 Apple Power Mac G4 (OSX 10.2, Absoft) 733 209 Apple Power Mac G4 (OSX 10.2, g77 3.3) 733 170 Compaq AlphaServer DS10 (Tru64 5.0) 466 106 SGI IndigoII R10K (Irix 6.5, MIPS) 195 280

BENCHMARK #5: Tinker Water Box Molecular Dynamics

The system consists of 216 AMOEBA flexible polarizable atomic multipole water molecules in a 18.643 Angstrom periodic box using regular Ewald summation for the electrostatics and a 12.0 Angstrom 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-OS-COMPILER TYPE MHz DYNAMICS

> Athlon XP 2400+ (RH 8.0, Intel) 2000 108 Athlon XP 2400+ (RH 8.0, PGI) 2000 104 Athlon XP 2400+ (RH 8.0, g77 3.2) 2000 128 Athlon Thunderbird (RH 8.0, Intel) 1400 165 Athlon Thunderbird (RH 8.0, PGI) 1400 158 Athlon Thunderbird (RH 8.0, g77 3.2) 1400 183 Athlon Classic (RH 8.0, Intel) 950 282 Athlon Classic (RH 8.0, PGI) 950 261 Athlon Classic (RH 8.0, g77 3.2) 950 307 Compaq Evo N610c P4 (RH 8.0, Intel) 2000 156 Compaq Evo N610c P4 (RH 8.0, PGI) 2000 191 Compaq Evo N610c P4 (RH 8.0, Absoft) 2000 226 Compaq Evo N610c P4 (RH 8.0, g77 3.2) 2000 243 Compaq Evo N610c P4 (WinXP, CVF 6.6) 2000 176 Compaq Evo N610c P4 (WinXP, g77 3.2) 2000 263 Apple Power Mac G4 (OSX 10.2, Absoft) 733 680 Apple Power Mac G4 (OSX 10.2, g77 3.3) 733 479 Compaq AlphaServer DS10 (Tru64 5.0) 466 358 SGI IndigoII R10K (Irix 6.5, MIPS) 195 868