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Merge pull request #47 from raimis/benchmarks
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Initial benchmark systems
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@PhilippThoelke
PhilippThoelke committed Nov 17, 2021
2 parents 552c4b2 + 4605efb commit 57b4d51
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8 changes: 8 additions & 0 deletions benchmarks/README.md
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# Benchmarks

A collection of scripts and systems for performance benchmarks.

## Systems

- `alaninde_dipeptide` -- a small peptide (22 atoms)
- `chignolin` -- 10-residue protein (166 atoms)
25 changes: 25 additions & 0 deletions benchmarks/systems/alanine_dipeptide.pdb
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MODEL 1
ATOM 1 H1 ACE 1 7.237 1.919 1.818 0.00 0.00 H
ATOM 2 CH3 ACE 1 6.510 2.680 2.100 0.00 0.00 C
ATOM 3 H2 ACE 1 5.615 2.573 1.487 0.00 0.00 H
ATOM 4 H3 ACE 1 6.940 3.670 1.944 0.00 0.00 H
ATOM 5 C ACE 1 6.114 2.545 3.572 0.00 0.00 C
ATOM 6 O ACE 1 6.604 1.661 4.271 0.00 0.00 O
ATOM 7 N ALA 2 5.226 3.427 4.035 0.00 0.00 N
ATOM 8 H ALA 2 4.919 4.090 3.339 0.00 0.00 H
ATOM 9 CA ALA 2 4.770 3.404 5.411 0.00 0.00 C
ATOM 10 HA ALA 2 4.323 2.518 5.594 0.00 0.00 H
ATOM 11 CB ALA 2 5.934 3.594 6.378 0.00 0.00 C
ATOM 12 HB1 ALA 2 5.580 3.823 7.284 0.00 0.00 H
ATOM 13 HB2 ALA 2 6.464 2.748 6.431 0.00 0.00 H
ATOM 14 HB3 ALA 2 6.520 4.334 6.052 0.00 0.00 H
ATOM 15 C ALA 2 3.763 4.515 5.672 0.00 0.00 C
ATOM 16 O ALA 2 3.436 5.285 4.772 0.00 0.00 O
ATOM 17 N NME 3 3.269 4.595 6.910 0.00 0.00 N
ATOM 18 H NME 3 3.570 3.936 7.613 0.00 0.00 H
ATOM 19 CH3 NME 3 2.303 5.607 7.286 0.00 0.00 C
ATOM 20 HH31 NME 3 2.081 6.236 6.424 0.00 0.00 H
ATOM 21 HH32 NME 3 1.387 5.126 7.629 0.00 0.00 H
ATOM 22 HH33 NME 3 2.713 6.221 8.087 0.00 0.00 H
ENDMDL
END
169 changes: 169 additions & 0 deletions benchmarks/systems/chignolin.pdb
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MODEL 1
ATOM 1 N TYR 1 17.733 6.661 8.939 0.00 0.00 N
ATOM 2 H1 TYR 1 17.331 7.009 8.080 0.00 0.00 H
ATOM 3 H2 TYR 1 18.593 6.178 8.722 0.00 0.00 H
ATOM 4 H3 TYR 1 17.730 7.404 9.623 0.00 0.00 H
ATOM 5 CA TYR 1 16.844 5.642 9.475 0.00 0.00 C
ATOM 6 HA TYR 1 17.381 4.696 9.545 0.00 0.00 H
ATOM 7 CB TYR 1 16.334 6.019 10.868 0.00 0.00 C
ATOM 8 HB2 TYR 1 15.585 6.801 10.745 0.00 0.00 H
ATOM 9 HB3 TYR 1 15.870 5.138 11.312 0.00 0.00 H
ATOM 10 CG TYR 1 17.434 6.516 11.771 0.00 0.00 C
ATOM 11 CD1 TYR 1 17.738 7.860 11.976 0.00 0.00 C
ATOM 12 HD1 TYR 1 17.158 8.625 11.460 0.00 0.00 H
ATOM 13 CE1 TYR 1 18.779 8.232 12.836 0.00 0.00 C
ATOM 14 HE1 TYR 1 19.019 9.274 13.050 0.00 0.00 H
ATOM 15 CZ TYR 1 19.486 7.221 13.453 0.00 0.00 C
ATOM 16 OH TYR 1 20.557 7.610 14.283 0.00 0.00 O
ATOM 17 HH TYR 1 20.674 8.562 14.324 0.00 0.00 H
ATOM 18 CE2 TYR 1 19.234 5.861 13.278 0.00 0.00 C
ATOM 19 HE2 TYR 1 19.800 5.064 13.760 0.00 0.00 H
ATOM 20 CD2 TYR 1 18.200 5.554 12.437 0.00 0.00 C
ATOM 21 HD2 TYR 1 17.935 4.512 12.256 0.00 0.00 H
ATOM 22 C TYR 1 15.638 5.548 8.553 0.00 0.00 C
ATOM 23 O TYR 1 15.299 6.592 7.990 0.00 0.00 O
ATOM 24 N TYR 2 14.977 4.420 8.405 0.00 0.00 N
ATOM 25 H TYR 2 15.441 3.583 8.820 0.00 0.00 H
ATOM 26 CA TYR 2 13.710 4.371 7.718 0.00 0.00 C
ATOM 27 HA TYR 2 13.657 5.146 7.082 0.00 0.00 H
ATOM 28 CB TYR 2 13.557 3.104 6.909 0.00 0.00 C
ATOM 29 HB2 TYR 2 13.706 2.316 7.527 0.00 0.00 H
ATOM 30 HB3 TYR 2 12.601 3.055 6.579 0.00 0.00 H
ATOM 31 CG TYR 2 14.462 2.950 5.732 0.00 0.00 C
ATOM 32 CD1 TYR 2 15.607 2.178 5.796 0.00 0.00 C
ATOM 33 HD1 TYR 2 15.850 1.718 6.653 0.00 0.00 H
ATOM 34 CE1 TYR 2 16.429 2.029 4.692 0.00 0.00 C
ATOM 35 HE1 TYR 2 17.267 1.459 4.769 0.00 0.00 H
ATOM 36 CZ TYR 2 16.138 2.637 3.479 0.00 0.00 C
ATOM 37 OH TYR 2 16.886 2.468 2.366 0.00 0.00 O
ATOM 38 HH TYR 2 16.527 3.040 1.625 0.00 0.00 H
ATOM 39 CE2 TYR 2 14.989 3.367 3.410 0.00 0.00 C
ATOM 40 HE2 TYR 2 14.715 3.793 2.528 0.00 0.00 H
ATOM 41 CD2 TYR 2 14.180 3.546 4.517 0.00 0.00 C
ATOM 42 HD2 TYR 2 13.362 4.126 4.434 0.00 0.00 H
ATOM 43 C TYR 2 12.576 4.509 8.722 0.00 0.00 C
ATOM 44 O TYR 2 12.576 3.947 9.788 0.00 0.00 O
ATOM 45 N ASP 3 11.574 5.296 8.327 0.00 0.00 N
ATOM 46 H ASP 3 11.720 5.730 7.385 0.00 0.00 H
ATOM 47 CA ASP 3 10.386 5.529 9.133 0.00 0.00 C
ATOM 48 HA ASP 3 10.685 5.636 10.089 0.00 0.00 H
ATOM 49 CB ASP 3 9.688 6.768 8.605 0.00 0.00 C
ATOM 50 HB2 ASP 3 10.359 7.511 8.585 0.00 0.00 H
ATOM 51 HB3 ASP 3 9.385 6.573 7.671 0.00 0.00 H
ATOM 52 CG ASP 3 8.521 7.184 9.424 0.00 0.00 C
ATOM 53 OD1 ASP 3 7.439 6.601 9.351 0.00 0.00 O
ATOM 54 OD2 ASP 3 8.763 8.187 10.213 0.00 0.00 O
ATOM 55 C ASP 3 9.443 4.319 9.099 0.00 0.00 C
ATOM 56 O ASP 3 9.203 3.794 8.012 0.00 0.00 O
ATOM 57 N PRO 4 8.935 3.879 10.227 0.00 0.00 N
ATOM 58 CD PRO 4 9.152 4.397 11.590 0.00 0.00 C
ATOM 59 HD2 PRO 4 8.977 5.379 11.620 0.00 0.00 H
ATOM 60 HD3 PRO 4 10.089 4.214 11.887 0.00 0.00 H
ATOM 61 CG PRO 4 8.155 3.629 12.387 0.00 0.00 C
ATOM 62 HG2 PRO 4 7.263 4.115 12.413 0.00 0.00 H
ATOM 63 HG3 PRO 4 8.464 3.529 13.350 0.00 0.00 H
ATOM 64 CB PRO 4 8.010 2.309 11.748 0.00 0.00 C
ATOM 65 HB2 PRO 4 7.121 1.902 11.932 0.00 0.00 H
ATOM 66 HB3 PRO 4 8.736 1.684 12.014 0.00 0.00 H
ATOM 67 CA PRO 4 8.132 2.650 10.238 0.00 0.00 C
ATOM 68 HA PRO 4 8.659 1.885 9.804 0.00 0.00 H
ATOM 69 C PRO 4 6.761 2.778 9.608 0.00 0.00 C
ATOM 70 O PRO 4 6.169 1.746 9.279 0.00 0.00 O
ATOM 71 N GLU 5 6.240 4.002 9.502 0.00 0.00 N
ATOM 72 H GLU 5 6.865 4.757 9.893 0.00 0.00 H
ATOM 73 CA GLU 5 4.949 4.279 8.913 0.00 0.00 C
ATOM 74 HA GLU 5 4.331 3.484 9.057 0.00 0.00 H
ATOM 75 CB GLU 5 4.195 5.411 9.665 0.00 0.00 C
ATOM 76 HB2 GLU 5 4.862 6.106 9.869 0.00 0.00 H
ATOM 77 HB3 GLU 5 3.495 5.737 9.055 0.00 0.00 H
ATOM 78 CG GLU 5 3.554 4.972 10.942 0.00 0.00 C
ATOM 79 HG2 GLU 5 4.263 4.544 11.520 0.00 0.00 H
ATOM 80 HG3 GLU 5 3.215 5.792 11.425 0.00 0.00 H
ATOM 81 CD GLU 5 2.404 4.002 10.868 0.00 0.00 C
ATOM 82 OE1 GLU 5 2.187 3.211 11.828 0.00 0.00 O
ATOM 83 OE2 GLU 5 1.661 4.057 9.868 0.00 0.00 O
ATOM 84 C GLU 5 5.041 4.582 7.437 0.00 0.00 C
ATOM 85 O GLU 5 4.167 4.140 6.654 0.00 0.00 O
ATOM 86 N THR 6 6.046 5.341 7.015 0.00 0.00 N
ATOM 87 H THR 6 6.755 5.569 7.734 0.00 0.00 H
ATOM 88 CA THR 6 6.109 5.796 5.642 0.00 0.00 C
ATOM 89 HA THR 6 5.207 5.633 5.206 0.00 0.00 H
ATOM 90 CB THR 6 6.420 7.280 5.525 0.00 0.00 C
ATOM 91 HB THR 6 6.435 7.542 4.539 0.00 0.00 H
ATOM 92 CG2 THR 6 5.445 8.142 6.327 0.00 0.00 C
ATOM 93 HG21 THR 6 5.950 8.682 7.002 0.00 0.00 H
ATOM 94 HG22 THR 6 4.955 8.759 5.709 0.00 0.00 H
ATOM 95 HG23 THR 6 4.786 7.554 6.799 0.00 0.00 H
ATOM 96 OG1 THR 6 7.711 7.524 6.069 0.00 0.00 O
ATOM 97 HG1 THR 6 7.737 7.279 7.046 0.00 0.00 H
ATOM 98 C THR 6 7.164 5.062 4.836 0.00 0.00 C
ATOM 99 O THR 6 7.149 5.123 3.601 0.00 0.00 O
ATOM 100 N GLY 7 8.125 4.375 5.452 0.00 0.00 N
ATOM 101 H GLY 7 8.057 4.396 6.499 0.00 0.00 H
ATOM 102 CA GLY 7 9.165 3.666 4.740 0.00 0.00 C
ATOM 103 HA2 GLY 7 9.649 3.040 5.394 0.00 0.00 H
ATOM 104 HA3 GLY 7 8.730 3.047 4.045 0.00 0.00 H
ATOM 105 C GLY 7 10.168 4.546 4.062 0.00 0.00 C
ATOM 106 O GLY 7 10.924 4.081 3.207 0.00 0.00 O
ATOM 107 N THR 8 10.271 5.794 4.396 0.00 0.00 N
ATOM 108 H THR 8 9.589 6.064 5.194 0.00 0.00 H
ATOM 109 CA THR 8 11.151 6.750 3.826 0.00 0.00 C
ATOM 110 HA THR 8 11.532 6.392 2.965 0.00 0.00 H
ATOM 111 CB THR 8 10.462 8.063 3.463 0.00 0.00 C
ATOM 112 HB THR 8 11.166 8.737 3.159 0.00 0.00 H
ATOM 113 CG2 THR 8 9.407 7.861 2.387 0.00 0.00 C
ATOM 114 HG21 THR 8 9.846 7.798 1.487 0.00 0.00 H
ATOM 115 HG22 THR 8 8.898 7.015 2.564 0.00 0.00 H
ATOM 116 HG23 THR 8 8.768 8.634 2.387 0.00 0.00 H
ATOM 117 OG1 THR 8 9.814 8.592 4.623 0.00 0.00 O
ATOM 118 HG1 THR 8 9.079 7.976 4.926 0.00 0.00 H
ATOM 119 C THR 8 12.328 7.016 4.775 0.00 0.00 C
ATOM 120 O THR 8 12.226 6.862 6.014 0.00 0.00 O
ATOM 121 N TRP 9 13.426 7.408 4.218 0.00 0.00 N
ATOM 122 H TRP 9 13.367 7.533 3.166 0.00 0.00 H
ATOM 123 CA TRP 9 14.671 7.670 4.942 0.00 0.00 C
ATOM 124 HA TRP 9 14.739 7.001 5.680 0.00 0.00 H
ATOM 125 CB TRP 9 15.833 7.594 4.008 0.00 0.00 C
ATOM 126 HB2 TRP 9 15.838 6.709 3.543 0.00 0.00 H
ATOM 127 HB3 TRP 9 15.773 8.327 3.330 0.00 0.00 H
ATOM 128 CG TRP 9 17.176 7.735 4.670 0.00 0.00 C
ATOM 129 CD1 TRP 9 17.933 8.837 4.761 0.00 0.00 C
ATOM 130 HD1 TRP 9 17.704 9.739 4.386 0.00 0.00 H
ATOM 131 NE1 TRP 9 19.089 8.561 5.451 0.00 0.00 N
ATOM 132 HE1 TRP 9 19.811 9.215 5.663 0.00 0.00 H
ATOM 133 CE2 TRP 9 19.087 7.235 5.801 0.00 0.00 C
ATOM 134 CZ2 TRP 9 20.034 6.482 6.482 0.00 0.00 C
ATOM 135 HZ2 TRP 9 20.900 6.918 6.785 0.00 0.00 H
ATOM 136 CH2 TRP 9 19.774 5.166 6.727 0.00 0.00 C
ATOM 137 HH2 TRP 9 20.425 4.607 7.230 0.00 0.00 H
ATOM 138 CZ3 TRP 9 18.585 4.583 6.273 0.00 0.00 C
ATOM 139 HZ3 TRP 9 18.412 3.621 6.440 0.00 0.00 H
ATOM 140 CE3 TRP 9 17.656 5.337 5.595 0.00 0.00 C
ATOM 141 HE3 TRP 9 16.797 4.903 5.278 0.00 0.00 H
ATOM 142 CD2 TRP 9 17.884 6.691 5.342 0.00 0.00 C
ATOM 143 C TRP 9 14.596 9.050 5.570 0.00 0.00 C
ATOM 144 O TRP 9 14.230 10.021 4.886 0.00 0.00 O
ATOM 145 N TYR 10 14.962 9.178 6.840 0.00 0.00 N
ATOM 146 H TYR 10 15.122 8.347 7.391 0.00 0.00 H
ATOM 147 CA TYR 10 15.044 10.457 7.495 0.00 0.00 C
ATOM 148 HA TYR 10 15.149 11.241 6.745 0.00 0.00 H
ATOM 149 CB TYR 10 13.771 10.743 8.337 0.00 0.00 C
ATOM 150 HB2 TYR 10 13.826 11.780 8.668 0.00 0.00 H
ATOM 151 HB3 TYR 10 12.896 10.610 7.701 0.00 0.00 H
ATOM 152 CG TYR 10 13.663 9.850 9.522 0.00 0.00 C
ATOM 153 CD1 TYR 10 14.108 10.198 10.801 0.00 0.00 C
ATOM 154 HD1 TYR 10 14.551 11.188 10.907 0.00 0.00 H
ATOM 155 CE1 TYR 10 14.013 9.375 11.883 0.00 0.00 C
ATOM 156 HE1 TYR 10 14.360 9.720 12.857 0.00 0.00 H
ATOM 157 CZ TYR 10 13.472 8.115 11.751 0.00 0.00 C
ATOM 158 OH TYR 10 13.408 7.305 12.829 0.00 0.00 O
ATOM 159 HH TYR 10 13.765 7.709 13.623 0.00 0.00 H
ATOM 160 CE2 TYR 10 13.027 7.737 10.505 0.00 0.00 C
ATOM 161 HE2 TYR 10 12.598 6.741 10.393 0.00 0.00 H
ATOM 162 CD2 TYR 10 13.112 8.576 9.417 0.00 0.00 C
ATOM 163 HD2 TYR 10 12.743 8.248 8.445 0.00 0.00 H
ATOM 164 C TYR 10 16.295 10.580 8.347 0.00 0.00 C
ATOM 165 O TYR 10 16.494 11.740 8.771 0.00 0.00 O
ATOM 166 OXT TYR 10 16.993 9.577 8.585 0.00 0.00 O
ENDMDL
END

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