From: Cezary Czaplewski Date: Mon, 29 Feb 2016 09:34:10 +0000 (+0100) Subject: ctest for minimization and microcanonical MD X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=448d3fa03a35e72321187b33bbc3a05b2ba01b3a ctest for minimization and microcanonical MD test of minimization of protein A compares final energy and SUMSL return code test of microcanonical MD of 1L2Y calculates average total energy and its standard deviation --- diff --git a/ctest/1L2Y.pdb b/ctest/1L2Y.pdb new file mode 100644 index 0000000..2e55ae8 --- /dev/null +++ b/ctest/1L2Y.pdb @@ -0,0 +1,306 @@ +ATOM 1 N ASN A 1 -8.901 4.127 -0.555 0.00 0.00 N +ATOM 2 CA ASN A 1 -8.608 3.135 -1.618 0.00 0.00 C +ATOM 3 C ASN A 1 -7.117 2.964 -1.897 0.00 0.00 C +ATOM 4 O ASN A 1 -6.634 1.849 -1.758 0.00 0.00 O +ATOM 5 CB ASN A 1 -9.437 3.396 -2.889 0.00 0.00 C +ATOM 6 CG ASN A 1 -10.915 3.130 -2.611 0.00 0.00 C +ATOM 7 OD1 ASN A 1 -11.269 2.700 -1.524 0.00 0.00 O +ATOM 8 ND2 ASN A 1 -11.806 3.406 -3.543 0.00 0.00 N +ATOM 9 1H ASN A 1 -8.330 3.957 0.261 0.00 0.00 H +ATOM 10 2H ASN A 1 -8.740 5.068 -0.889 0.00 0.00 H +ATOM 11 3H ASN A 1 -9.877 4.041 -0.293 0.00 0.00 H +ATOM 12 HA ASN A 1 -8.930 2.162 -1.239 0.00 0.00 H +ATOM 13 1HB ASN A 1 -9.310 4.417 -3.193 0.00 0.00 H +ATOM 14 2HB ASN A 1 -9.108 2.719 -3.679 0.00 0.00 H +ATOM 15 1HD2 ASN A 1 -11.572 3.791 -4.444 0.00 0.00 H +ATOM 16 2HD2 ASN A 1 -12.757 3.183 -3.294 0.00 0.00 H +ATOM 17 N LEU A 2 -6.379 4.031 -2.228 0.00 0.00 N +ATOM 18 CA LEU A 2 -4.923 4.002 -2.452 0.00 0.00 C +ATOM 19 C LEU A 2 -4.136 3.187 -1.404 0.00 0.00 C +ATOM 20 O LEU A 2 -3.391 2.274 -1.760 0.00 0.00 O +ATOM 21 CB LEU A 2 -4.411 5.450 -2.619 0.00 0.00 C +ATOM 22 CG LEU A 2 -4.795 6.450 -1.495 0.00 0.00 C +ATOM 23 CD1 LEU A 2 -3.612 6.803 -0.599 0.00 0.00 C +ATOM 24 CD2 LEU A 2 -5.351 7.748 -2.084 0.00 0.00 C +ATOM 25 H LEU A 2 -6.821 4.923 -2.394 0.00 0.00 H +ATOM 26 HA LEU A 2 -4.750 3.494 -3.403 0.00 0.00 H +ATOM 27 1HB LEU A 2 -3.340 5.414 -2.672 0.00 0.00 H +ATOM 28 2HB LEU A 2 -4.813 5.817 -3.564 0.00 0.00 H +ATOM 29 HG LEU A 2 -5.568 6.022 -0.858 0.00 0.00 H +ATOM 30 1HD1 LEU A 2 -3.207 5.905 -0.146 0.00 0.00 H +ATOM 31 2HD1 LEU A 2 -2.841 7.304 -1.183 0.00 0.00 H +ATOM 32 3HD1 LEU A 2 -3.929 7.477 0.197 0.00 0.00 H +ATOM 33 1HD2 LEU A 2 -4.607 8.209 -2.736 0.00 0.00 H +ATOM 34 2HD2 LEU A 2 -6.255 7.544 -2.657 0.00 0.00 H +ATOM 35 3HD2 LEU A 2 -5.592 8.445 -1.281 0.00 0.00 H +ATOM 36 N TYR A 3 -4.354 3.455 -0.111 0.00 0.00 N +ATOM 37 CA TYR A 3 -3.690 2.738 0.981 0.00 0.00 C +ATOM 38 C TYR A 3 -4.102 1.256 1.074 0.00 0.00 C +ATOM 39 O TYR A 3 -3.291 0.409 1.442 0.00 0.00 O +ATOM 40 CB TYR A 3 -3.964 3.472 2.302 0.00 0.00 C +ATOM 41 CG TYR A 3 -2.824 3.339 3.290 0.00 0.00 C +ATOM 42 CD1 TYR A 3 -1.820 4.326 3.332 0.00 0.00 C +ATOM 43 CD2 TYR A 3 -2.746 2.217 4.138 0.00 0.00 C +ATOM 44 CE1 TYR A 3 -0.725 4.185 4.205 0.00 0.00 C +ATOM 45 CE2 TYR A 3 -1.657 2.076 5.018 0.00 0.00 C +ATOM 46 CZ TYR A 3 -0.639 3.053 5.043 0.00 0.00 C +ATOM 47 OH TYR A 3 0.433 2.881 5.861 0.00 0.00 O +ATOM 48 H TYR A 3 -4.934 4.245 0.120 0.00 0.00 H +ATOM 49 HA TYR A 3 -2.615 2.768 0.796 0.00 0.00 H +ATOM 50 1HB TYR A 3 -4.117 4.513 2.091 0.00 0.00 H +ATOM 51 2HB TYR A 3 -4.886 3.096 2.750 0.00 0.00 H +ATOM 52 HD1 TYR A 3 -1.877 5.200 2.695 0.00 0.00 H +ATOM 53 HD2 TYR A 3 -3.513 1.456 4.101 0.00 0.00 H +ATOM 54 HE1 TYR A 3 0.033 4.952 4.233 0.00 0.00 H +ATOM 55 HE2 TYR A 3 -1.576 1.221 5.669 0.00 0.00 H +ATOM 56 HH TYR A 3 1.187 3.395 5.567 0.00 0.00 H +ATOM 57 N ILE A 4 -5.342 0.925 0.689 0.00 0.00 N +ATOM 58 CA ILE A 4 -5.857 -0.449 0.613 0.00 0.00 C +ATOM 59 C ILE A 4 -5.089 -1.221 -0.470 0.00 0.00 C +ATOM 60 O ILE A 4 -4.621 -2.334 -0.226 0.00 0.00 O +ATOM 61 CB ILE A 4 -7.386 -0.466 0.343 0.00 0.00 C +ATOM 62 CG1 ILE A 4 -8.197 0.540 1.197 0.00 0.00 C +ATOM 63 CG2 ILE A 4 -7.959 -1.884 0.501 0.00 0.00 C +ATOM 64 CD1 ILE A 4 -8.019 0.412 2.715 0.00 0.00 C +ATOM 65 H ILE A 4 -5.906 1.656 0.283 0.00 0.00 H +ATOM 66 HA ILE A 4 -5.670 -0.941 1.568 0.00 0.00 H +ATOM 67 HB ILE A 4 -7.554 -0.192 -0.697 0.00 0.00 H +ATOM 68 1HG1 ILE A 4 -7.900 1.531 0.912 0.00 0.00 H +ATOM 69 2HG1 ILE A 4 -9.257 0.424 0.964 0.00 0.00 H +ATOM 70 1HG2 ILE A 4 -7.509 -2.555 -0.232 0.00 0.00 H +ATOM 71 2HG2 ILE A 4 -7.759 -2.271 1.501 0.00 0.00 H +ATOM 72 3HG2 ILE A 4 -9.036 -1.871 0.332 0.00 0.00 H +ATOM 73 1HD1 ILE A 4 -8.306 -0.585 3.049 0.00 0.00 H +ATOM 74 2HD1 ILE A 4 -6.983 0.606 2.995 0.00 0.00 H +ATOM 75 3HD1 ILE A 4 -8.656 1.144 3.213 0.00 0.00 H +ATOM 76 N GLN A 5 -4.907 -0.601 -1.645 0.00 0.00 N +ATOM 77 CA GLN A 5 -4.122 -1.167 -2.743 0.00 0.00 C +ATOM 78 C GLN A 5 -2.629 -1.321 -2.390 0.00 0.00 C +ATOM 79 O GLN A 5 -1.986 -2.240 -2.884 0.00 0.00 O +ATOM 80 CB GLN A 5 -4.292 -0.313 -4.013 0.00 0.00 C +ATOM 81 CG GLN A 5 -4.244 -1.171 -5.290 0.00 0.00 C +ATOM 82 CD GLN A 5 -5.576 -1.860 -5.585 0.00 0.00 C +ATOM 83 OE1 GLN A 5 -5.769 -3.044 -5.335 0.00 0.00 O +ATOM 84 NE2 GLN A 5 -6.532 -1.146 -6.152 0.00 0.00 N +ATOM 85 H GLN A 5 -5.327 0.318 -1.763 0.00 0.00 H +ATOM 86 HA GLN A 5 -4.517 -2.162 -2.940 0.00 0.00 H +ATOM 87 1HB GLN A 5 -5.238 0.191 -3.969 0.00 0.00 H +ATOM 88 2HB GLN A 5 -3.492 0.429 -4.053 0.00 0.00 H +ATOM 89 1HG GLN A 5 -3.993 -0.539 -6.120 0.00 0.00 H +ATOM 90 2HG GLN A 5 -3.458 -1.923 -5.205 0.00 0.00 H +ATOM 91 1HE2 GLN A 5 -6.389 -0.184 -6.408 0.00 0.00 H +ATOM 92 2HE2 GLN A 5 -7.392 -1.635 -6.335 0.00 0.00 H +ATOM 93 N TRP A 6 -2.074 -0.459 -1.528 0.00 0.00 N +ATOM 94 CA TRP A 6 -0.716 -0.631 -0.993 0.00 0.00 C +ATOM 95 C TRP A 6 -0.631 -1.766 0.044 0.00 0.00 C +ATOM 96 O TRP A 6 0.295 -2.579 -0.004 0.00 0.00 O +ATOM 97 CB TRP A 6 -0.221 0.703 -0.417 0.00 0.00 C +ATOM 98 CG TRP A 6 1.148 0.652 0.194 0.00 0.00 C +ATOM 99 CD1 TRP A 6 2.319 0.664 -0.482 0.00 0.00 C +ATOM 100 CD2 TRP A 6 1.508 0.564 1.606 0.00 0.00 C +ATOM 101 NE1 TRP A 6 3.371 0.560 0.411 0.00 0.00 N +ATOM 102 CE2 TRP A 6 2.928 0.515 1.710 0.00 0.00 C +ATOM 103 CE3 TRP A 6 0.779 0.524 2.812 0.00 0.00 C +ATOM 104 CZ2 TRP A 6 3.599 0.445 2.938 0.00 0.00 C +ATOM 105 CZ3 TRP A 6 1.439 0.433 4.053 0.00 0.00 C +ATOM 106 CH2 TRP A 6 2.842 0.407 4.120 0.00 0.00 C +ATOM 107 H TRP A 6 -2.624 0.343 -1.242 0.00 0.00 H +ATOM 108 HA TRP A 6 -0.052 -0.908 -1.813 0.00 0.00 H +ATOM 109 1HB TRP A 6 -0.206 1.425 -1.211 0.00 0.00 H +ATOM 110 2HB TRP A 6 -0.921 1.044 0.344 0.00 0.00 H +ATOM 111 HD1 TRP A 6 2.412 0.733 -1.558 0.00 0.00 H +ATOM 112 HE1 TRP A 6 4.360 0.536 0.156 0.00 0.00 H +ATOM 113 HE3 TRP A 6 -0.299 0.571 2.773 0.00 0.00 H +ATOM 114 HZ2 TRP A 6 4.679 0.418 2.961 0.00 0.00 H +ATOM 115 HZ3 TRP A 6 0.862 0.400 4.966 0.00 0.00 H +ATOM 116 HH2 TRP A 6 3.334 0.360 5.081 0.00 0.00 H +ATOM 117 N LEU A 7 -1.600 -1.860 0.967 0.00 0.00 N +ATOM 118 CA LEU A 7 -1.641 -2.932 1.963 0.00 0.00 C +ATOM 119 C LEU A 7 -1.847 -4.319 1.342 0.00 0.00 C +ATOM 120 O LEU A 7 -1.144 -5.248 1.742 0.00 0.00 O +ATOM 121 CB LEU A 7 -2.710 -2.645 3.033 0.00 0.00 C +ATOM 122 CG LEU A 7 -2.301 -1.579 4.069 0.00 0.00 C +ATOM 123 CD1 LEU A 7 -3.475 -1.323 5.018 0.00 0.00 C +ATOM 124 CD2 LEU A 7 -1.093 -2.007 4.914 0.00 0.00 C +ATOM 125 H LEU A 7 -2.316 -1.137 0.994 0.00 0.00 H +ATOM 126 HA LEU A 7 -0.666 -2.978 2.445 0.00 0.00 H +ATOM 127 1HB LEU A 7 -3.600 -2.308 2.537 0.00 0.00 H +ATOM 128 2HB LEU A 7 -2.921 -3.571 3.572 0.00 0.00 H +ATOM 129 HG LEU A 7 -2.061 -0.649 3.560 0.00 0.00 H +ATOM 130 1HD1 LEU A 7 -4.343 -0.992 4.449 0.00 0.00 H +ATOM 131 2HD1 LEU A 7 -3.725 -2.237 5.560 0.00 0.00 H +ATOM 132 3HD1 LEU A 7 -3.211 -0.549 5.739 0.00 0.00 H +ATOM 133 1HD2 LEU A 7 -1.270 -2.989 5.354 0.00 0.00 H +ATOM 134 2HD2 LEU A 7 -0.195 -2.045 4.300 0.00 0.00 H +ATOM 135 3HD2 LEU A 7 -0.922 -1.286 5.712 0.00 0.00 H +ATOM 136 N LYS A 8 -2.753 -4.481 0.360 0.00 0.00 N +ATOM 137 CA LYS A 8 -3.024 -5.791 -0.269 0.00 0.00 C +ATOM 138 C LYS A 8 -1.796 -6.427 -0.937 0.00 0.00 C +ATOM 139 O LYS A 8 -1.719 -7.648 -1.030 0.00 0.00 O +ATOM 140 CB LYS A 8 -4.224 -5.697 -1.232 0.00 0.00 C +ATOM 141 CG LYS A 8 -3.930 -5.009 -2.577 0.00 0.00 C +ATOM 142 CD LYS A 8 -3.682 -5.986 -3.736 0.00 0.00 C +ATOM 143 CE LYS A 8 -3.494 -5.199 -5.039 0.00 0.00 C +ATOM 144 NZ LYS A 8 -4.563 -5.483 -6.023 0.00 0.00 N +ATOM 145 H LYS A 8 -3.321 -3.675 0.097 0.00 0.00 H +ATOM 146 HA LYS A 8 -3.309 -6.478 0.529 0.00 0.00 H +ATOM 147 1HB LYS A 8 -4.565 -6.694 -1.436 0.00 0.00 H +ATOM 148 2HB LYS A 8 -5.019 -5.143 -0.731 0.00 0.00 H +ATOM 149 1HG LYS A 8 -4.769 -4.390 -2.830 0.00 0.00 H +ATOM 150 2HG LYS A 8 -3.062 -4.368 -2.469 0.00 0.00 H +ATOM 151 1HD LYS A 8 -2.799 -6.562 -3.536 0.00 0.00 H +ATOM 152 2HD LYS A 8 -4.524 -6.674 -3.818 0.00 0.00 H +ATOM 153 1HE LYS A 8 -3.502 -4.150 -4.813 0.00 0.00 H +ATOM 154 2HE LYS A 8 -2.511 -5.439 -5.457 0.00 0.00 H +ATOM 155 1HZ LYS A 8 -4.621 -6.474 -6.211 0.00 0.00 H +ATOM 156 2HZ LYS A 8 -5.442 -5.124 -5.657 0.00 0.00 H +ATOM 157 3HZ LYS A 8 -4.382 -4.983 -6.881 0.00 0.00 H +ATOM 158 N ASP A 9 -0.828 -5.607 -1.355 0.00 0.00 N +ATOM 159 CA ASP A 9 0.466 -6.016 -1.905 0.00 0.00 C +ATOM 160 C ASP A 9 1.481 -6.464 -0.832 0.00 0.00 C +ATOM 161 O ASP A 9 2.545 -6.971 -1.194 0.00 0.00 O +ATOM 162 CB ASP A 9 1.033 -4.839 -2.724 0.00 0.00 C +ATOM 163 CG ASP A 9 0.672 -4.906 -4.210 0.00 0.00 C +ATOM 164 OD1 ASP A 9 -0.532 -5.051 -4.522 0.00 0.00 O +ATOM 165 OD2 ASP A 9 1.627 -4.815 -5.017 0.00 0.00 O +ATOM 166 H ASP A 9 -1.010 -4.616 -1.291 0.00 0.00 H +ATOM 167 HA ASP A 9 0.319 -6.867 -2.574 0.00 0.00 H +ATOM 168 1HB ASP A 9 0.644 -3.924 -2.320 0.00 0.00 H +ATOM 169 2HB ASP A 9 2.116 -4.837 -2.650 0.00 0.00 H +ATOM 170 N GLY A 10 1.185 -6.278 0.464 0.00 0.00 N +ATOM 171 CA GLY A 10 2.060 -6.618 1.593 0.00 0.00 C +ATOM 172 C GLY A 10 2.628 -5.412 2.353 0.00 0.00 C +ATOM 173 O GLY A 10 3.496 -5.594 3.208 0.00 0.00 O +ATOM 174 H GLY A 10 0.265 -5.908 0.693 0.00 0.00 H +ATOM 175 1HA GLY A 10 1.486 -7.214 2.304 0.00 0.00 H +ATOM 176 2HA GLY A 10 2.897 -7.228 1.252 0.00 0.00 H +ATOM 177 N GLY A 11 2.172 -4.187 2.055 0.00 0.00 N +ATOM 178 CA GLY A 11 2.626 -2.967 2.723 0.00 0.00 C +ATOM 179 C GLY A 11 4.157 -2.802 2.654 0.00 0.00 C +ATOM 180 O GLY A 11 4.710 -2.829 1.551 0.00 0.00 O +ATOM 181 H GLY A 11 1.481 -4.089 1.319 0.00 0.00 H +ATOM 182 1HA GLY A 11 2.164 -2.109 2.237 0.00 0.00 H +ATOM 183 2HA GLY A 11 2.280 -2.997 3.753 0.00 0.00 H +ATOM 184 N PRO A 12 4.871 -2.651 3.794 0.00 0.00 N +ATOM 185 CA PRO A 12 6.333 -2.533 3.806 0.00 0.00 C +ATOM 186 C PRO A 12 7.058 -3.729 3.165 0.00 0.00 C +ATOM 187 O PRO A 12 8.139 -3.562 2.601 0.00 0.00 O +ATOM 188 CB PRO A 12 6.740 -2.387 5.279 0.00 0.00 C +ATOM 189 CG PRO A 12 5.460 -1.952 5.987 0.00 0.00 C +ATOM 190 CD PRO A 12 4.362 -2.615 5.160 0.00 0.00 C +ATOM 191 HA PRO A 12 6.611 -1.626 3.267 0.00 0.00 H +ATOM 192 1HB PRO A 12 7.091 -3.323 5.670 0.00 0.00 H +ATOM 193 2HB PRO A 12 7.531 -1.647 5.403 0.00 0.00 H +ATOM 194 1HG PRO A 12 5.443 -2.302 7.001 0.00 0.00 H +ATOM 195 2HG PRO A 12 5.358 -0.867 5.929 0.00 0.00 H +ATOM 196 1HD PRO A 12 4.173 -3.609 5.516 0.00 0.00 H +ATOM 197 2HD PRO A 12 3.440 -2.042 5.246 0.00 0.00 H +ATOM 198 N SER A 13 6.463 -4.929 3.205 0.00 0.00 N +ATOM 199 CA SER A 13 7.049 -6.179 2.704 0.00 0.00 C +ATOM 200 C SER A 13 6.897 -6.369 1.185 0.00 0.00 C +ATOM 201 O SER A 13 7.025 -7.488 0.697 0.00 0.00 O +ATOM 202 CB SER A 13 6.458 -7.371 3.472 0.00 0.00 C +ATOM 203 OG SER A 13 6.763 -7.264 4.850 0.00 0.00 O +ATOM 204 H SER A 13 5.535 -4.999 3.613 0.00 0.00 H +ATOM 205 HA SER A 13 8.121 -6.159 2.903 0.00 0.00 H +ATOM 206 1HB SER A 13 5.393 -7.382 3.344 0.00 0.00 H +ATOM 207 2HB SER A 13 6.880 -8.302 3.093 0.00 0.00 H +ATOM 208 HG SER A 13 7.707 -7.394 4.970 0.00 0.00 H +ATOM 209 N SER A 14 6.637 -5.290 0.434 0.00 0.00 N +ATOM 210 CA SER A 14 6.389 -5.315 -1.015 0.00 0.00 C +ATOM 211 C SER A 14 7.332 -4.405 -1.823 0.00 0.00 C +ATOM 212 O SER A 14 7.082 -4.123 -2.993 0.00 0.00 O +ATOM 213 CB SER A 14 4.914 -4.993 -1.265 0.00 0.00 C +ATOM 214 OG SER A 14 4.431 -5.743 -2.358 0.00 0.00 O +ATOM 215 H SER A 14 6.509 -4.415 0.930 0.00 0.00 H +ATOM 216 HA SER A 14 6.562 -6.329 -1.378 0.00 0.00 H +ATOM 217 1HB SER A 14 4.344 -5.236 -0.389 0.00 0.00 H +ATOM 218 2HB SER A 14 4.778 -3.934 -1.457 0.00 0.00 H +ATOM 219 HG SER A 14 3.714 -6.324 -1.987 0.00 0.00 H +ATOM 220 N GLY A 15 8.419 -3.920 -1.202 0.00 0.00 N +ATOM 221 CA GLY A 15 9.451 -3.116 -1.870 0.00 0.00 C +ATOM 222 C GLY A 15 8.984 -1.725 -2.316 0.00 0.00 C +ATOM 223 O GLY A 15 9.539 -1.177 -3.267 0.00 0.00 O +ATOM 224 H GLY A 15 8.573 -4.210 -0.246 0.00 0.00 H +ATOM 225 1HA GLY A 15 10.297 -2.987 -1.194 0.00 0.00 H +ATOM 226 2HA GLY A 15 9.805 -3.652 -2.752 0.00 0.00 H +ATOM 227 N ARG A 16 7.956 -1.164 -1.660 0.00 0.00 N +ATOM 228 CA ARG A 16 7.289 0.084 -2.054 0.00 0.00 C +ATOM 229 C ARG A 16 6.855 0.916 -0.829 0.00 0.00 C +ATOM 230 O ARG A 16 6.222 0.366 0.076 0.00 0.00 O +ATOM 231 CB ARG A 16 6.110 -0.243 -2.994 0.00 0.00 C +ATOM 232 CG ARG A 16 5.046 -1.171 -2.378 0.00 0.00 C +ATOM 233 CD ARG A 16 3.923 -1.592 -3.338 0.00 0.00 C +ATOM 234 NE ARG A 16 4.251 -2.811 -4.100 0.00 0.00 N +ATOM 235 CZ ARG A 16 4.859 -2.914 -5.274 0.00 0.00 C +ATOM 236 NH1 ARG A 16 5.289 -1.864 -5.937 0.00 0.00 N +ATOM 237 NH2 ARG A 16 5.035 -4.095 -5.809 0.00 0.00 N +ATOM 238 H ARG A 16 7.579 -1.676 -0.874 0.00 0.00 H +ATOM 239 HA ARG A 16 8.009 0.663 -2.630 0.00 0.00 H +ATOM 240 1HB ARG A 16 5.634 0.678 -3.269 0.00 0.00 H +ATOM 241 2HB ARG A 16 6.524 -0.720 -3.880 0.00 0.00 H +ATOM 242 1HG ARG A 16 5.538 -2.059 -2.031 0.00 0.00 H +ATOM 243 2HG ARG A 16 4.579 -0.652 -1.549 0.00 0.00 H +ATOM 244 1HD ARG A 16 3.033 -1.774 -2.766 0.00 0.00 H +ATOM 245 2HD ARG A 16 3.669 -0.765 -4.003 0.00 0.00 H +ATOM 246 HE ARG A 16 3.963 -3.694 -3.698 0.00 0.00 H +ATOM 247 1HH1 ARG A 16 5.150 -0.962 -5.521 0.00 0.00 H +ATOM 248 2HH1 ARG A 16 5.761 -1.962 -6.815 0.00 0.00 H +ATOM 249 1HH2 ARG A 16 4.649 -4.894 -5.327 0.00 0.00 H +ATOM 250 2HH2 ARG A 16 5.508 -4.205 -6.684 0.00 0.00 H +ATOM 251 N PRO A 17 7.156 2.230 -0.780 0.00 0.00 N +ATOM 252 CA PRO A 17 6.782 3.088 0.345 0.00 0.00 C +ATOM 253 C PRO A 17 5.261 3.331 0.395 0.00 0.00 C +ATOM 254 O PRO A 17 4.586 3.165 -0.624 0.00 0.00 O +ATOM 255 CB PRO A 17 7.554 4.394 0.119 0.00 0.00 C +ATOM 256 CG PRO A 17 7.677 4.474 -1.401 0.00 0.00 C +ATOM 257 CD PRO A 17 7.820 3.010 -1.816 0.00 0.00 C +ATOM 258 HA PRO A 17 7.107 2.628 1.279 0.00 0.00 H +ATOM 259 1HB PRO A 17 7.009 5.234 0.505 0.00 0.00 H +ATOM 260 2HB PRO A 17 8.548 4.308 0.561 0.00 0.00 H +ATOM 261 1HG PRO A 17 6.800 4.914 -1.836 0.00 0.00 H +ATOM 262 2HG PRO A 17 8.540 5.066 -1.707 0.00 0.00 H +ATOM 263 1HD PRO A 17 7.349 2.844 -2.766 0.00 0.00 H +ATOM 264 2HD PRO A 17 8.876 2.739 -1.855 0.00 0.00 H +ATOM 265 N PRO A 18 4.710 3.739 1.555 0.00 0.00 N +ATOM 266 CA PRO A 18 3.287 4.031 1.686 0.00 0.00 C +ATOM 267 C PRO A 18 2.901 5.305 0.913 0.00 0.00 C +ATOM 268 O PRO A 18 3.684 6.256 0.871 0.00 0.00 O +ATOM 269 CB PRO A 18 3.035 4.190 3.187 0.00 0.00 C +ATOM 270 CG PRO A 18 4.385 4.655 3.729 0.00 0.00 C +ATOM 271 CD PRO A 18 5.393 3.949 2.823 0.00 0.00 C +ATOM 272 HA PRO A 18 2.719 3.181 1.316 0.00 0.00 H +ATOM 273 1HB PRO A 18 2.274 4.924 3.372 0.00 0.00 H +ATOM 274 2HB PRO A 18 2.781 3.223 3.618 0.00 0.00 H +ATOM 275 1HG PRO A 18 4.482 5.721 3.654 0.00 0.00 H +ATOM 276 2HG PRO A 18 4.518 4.377 4.775 0.00 0.00 H +ATOM 277 1HD PRO A 18 6.262 4.562 2.682 0.00 0.00 H +ATOM 278 2HD PRO A 18 5.662 2.983 3.253 0.00 0.00 H +ATOM 279 N PRO A 19 1.688 5.360 0.336 0.00 0.00 N +ATOM 280 CA PRO A 19 1.185 6.543 -0.353 0.00 0.00 C +ATOM 281 C PRO A 19 0.715 7.607 0.655 0.00 0.00 C +ATOM 282 O PRO A 19 -0.124 7.324 1.513 0.00 0.00 O +ATOM 283 CB PRO A 19 0.048 6.014 -1.229 0.00 0.00 C +ATOM 284 CG PRO A 19 -0.519 4.852 -0.412 0.00 0.00 C +ATOM 285 CD PRO A 19 0.716 4.275 0.272 0.00 0.00 C +ATOM 286 HA PRO A 19 1.961 6.966 -0.991 0.00 0.00 H +ATOM 287 1HB PRO A 19 -0.697 6.770 -1.389 0.00 0.00 H +ATOM 288 2HB PRO A 19 0.463 5.630 -2.162 0.00 0.00 H +ATOM 289 1HG PRO A 19 -1.232 5.201 0.310 0.00 0.00 H +ATOM 290 2HG PRO A 19 -1.019 4.114 -1.041 0.00 0.00 H +ATOM 291 1HD PRO A 19 0.470 3.937 1.260 0.00 0.00 H +ATOM 292 2HD PRO A 19 1.121 3.461 -0.329 0.00 0.00 H +ATOM 293 N SER A 20 1.271 8.822 0.549 0.00 0.00 N +ATOM 294 CA SER A 20 0.852 10.027 1.285 0.00 0.00 C +ATOM 295 C SER A 20 -0.406 10.657 0.683 0.00 0.00 C +ATOM 296 O SER A 20 -0.387 10.916 -0.540 0.00 0.00 O +ATOM 297 CB SER A 20 1.972 11.071 1.284 0.00 0.00 C +ATOM 298 OG SER A 20 3.120 10.541 1.911 0.00 0.00 O +ATOM 299 OXT SER A 20 -1.341 10.903 1.473 0.00 0.00 O +ATOM 300 H SER A 20 1.969 8.961 -0.165 0.00 0.00 H +ATOM 301 HA SER A 20 0.601 9.760 2.310 0.00 0.00 H +ATOM 302 1HB SER A 20 2.210 11.338 0.272 0.00 0.00 H +ATOM 303 2HB SER A 20 1.636 11.959 1.824 0.00 0.00 H +ATOM 304 HG SER A 20 2.831 10.040 2.676 0.00 0.00 H +TER 305 SER A 20 +END diff --git a/ctest/1l2y_micro.inp b/ctest/1l2y_micro.inp new file mode 100644 index 0000000..2c9162b --- /dev/null +++ b/ctest/1l2y_micro.inp @@ -0,0 +1,27 @@ +1L2Y microcanonical simulation with VTS algorithm in ff_1l2y +SEED=-3059743 PDBREF MD RESCALE_MODE=2 +nstep=100000 ntwe=1000 ntwx=10000 dt=0.01 damax=20.0 dvmax=20.0 lang=0 & +t_bath=300 reset_vel=0 PRINT_COMPON +WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 & +WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 & +WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 & +WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 & +CUTOFF=7.00000 WCORR4=0.00000 +1L2Y.pdb +22 + D ASN LEU TYR ILE GLN TRP LEU LYS ASP GLY GLY PRO SER SER GLY ARG PRO PRO PRO + SER D + 0 + 0 + 118.4740 91.7823 90.3404 89.3388 90.2688 90.5528 90.2608 91.8517 + 91.2516 112.6457 114.2855 93.3110 94.0115 113.7225 94.1935 122.6596 + 117.6789 115.7586 93.9337 117.7525 + -102.4154 63.8918 53.6672 44.5801 45.7047 51.3142 45.4942 65.8300 + -69.7204 -63.5184 -78.1774 56.7999 138.6359 -83.5800 61.1299 -80.0117 + -107.6271 -138.3675 46.2456 + 111.0437 140.0186 119.7331 146.2523 117.2478 139.8052 138.2821 132.6488 + 141.1706 180.0000 180.0000 128.9951 136.7308 122.7588 180.0000 87.7280 + 116.1119 141.5865 95.8012 143.6198 + -86.0387 -46.9729 113.9184 -93.8597 -118.2335 49.5995 -148.0897 -135.5996 + -121.1027 180.0000 180.0000 -152.5007 -154.1805 -145.3740 180.0000 -103.5827 + -122.4221 -157.5917 -96.8194 -130.8054 diff --git a/ctest/prota_MIN_CART.inp b/ctest/prota_MIN_CART.inp new file mode 100644 index 0000000..df0c2b3 --- /dev/null +++ b/ctest/prota_MIN_CART.inp @@ -0,0 +1,12 @@ +Test energii - 1bdd - pdbstart +SEED=-3059743 minimize pdbstart pdbref refstr rescale_mode=2 cart overlap & +nosearchsc +print_min_ini print_min_res print_min_stat MAXMIN=10000 MAXFUN=15000 +WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 & +WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 & +WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 & +WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 & +CUTOFF=7.00000 WCORR4=0.00000 +prota.pdb + 0 + 0 diff --git a/ctest/prota_unres_energy_check.sh b/ctest/prota_unres_energy_check.sh index e8107d7..3cd5b16 100755 --- a/ctest/prota_unres_energy_check.sh +++ b/ctest/prota_unres_energy_check.sh @@ -6,10 +6,48 @@ #---------------------------------------- # variables -extremediff="10000.0" # extreme energy difference, comething went terribly wrong -expectenergy="-56066670.000000" # expected total energy -cutoffdiff="0.1" # energy cutoff variation - more then this rises warning -file=$1 # Output file to search energy value from +if [[ "$2" =~ "MPI" ]]; then + file=$1.out_GB000 + file_stat=$1_GB000.stat +else + file=$1.out_GB # Output file to search energy value from + file_stat=$1_GB.stat +fi + +if [ "$1" == "prota_ENE" ]; then + extremediff="10000.0" # extreme energy difference, comething went terribly wrong + expectenergy="-56066670.000000" # expected total energy + cutoffdiff="0.1" # energy cutoff variation - more then this rises warning +elif [ "$1" == "prota_MIN_CART" ]; then + extremediff="10.0" # extreme energy difference, comething went terribly wrong + expectenergy="123.8713" # expected total energy + cutoffdiff="0.1" # energy cutoff variation - more then this rises warning + + sumsl_return=`grep SUMSL $file|awk '{print $4}'` + echo 'SUMSL return code' $sumsl_return + if [ "$sumsl_return" != "4" ]; then + echo 'ERROR = SUMSL return code' $sumsl_return 'is not 4' + exit 1 + fi +elif [ "$1" == "1l2y_micro" ]; then + stat=`awk '{if ( $1 != "#" ) {n++;a=a+$5;a2=a2+$5^2}}END{print a/n,sqrt((a2-a^2/n)/n)}' $file_stat` + array=(${stat// / }) + echo 'average total energy ' ${array[0]} + echo 'standard deviation ' ${array[1]} + if [ `echo "a=${array[0]}-103.162;if(0>a)a*=-1;a>5.0"|bc -l` != "0" ]; then + echo 'difference ' `echo "a=${array[0]}-103.162;if(0>a)a*=-1;a"|bc -l` 'from reference ave etot 103.162 greater than 5.0' + exit 1 + elif [ `echo "a=${array[1]};a>0.01"|bc -l` != "0" ]; then + echo 'standard deviation greater than 0.01' + exit 1 + else + exit 0 + fi +else + exit 1 +fi + + function floating(){ echo $1 | sed -e 's/[eE]+/*10^/' @@ -26,7 +64,7 @@ if [ ! -f $file ]; then fi # Check if energy value is not a number -grepene=`grep ETOT $file| awk '{print $2}'` +grepene=`grep ETOT $file|tail -1| awk '{print $2}'` if [[ $grepene == "NaN" ]]; then echo "CRITICAL: energy is NaN" exit 2 diff --git a/source/unres/src_MD/CMakeLists.txt b/source/unres/src_MD/CMakeLists.txt index 78ffb5c..77d4834 100644 --- a/source/unres/src_MD/CMakeLists.txt +++ b/source/unres/src_MD/CMakeLists.txt @@ -388,19 +388,21 @@ FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/prota.pdb FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/prota_ENE.inp DESTINATION ${CMAKE_CURRENT_BINARY_DIR} ) +FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/prota_MIN_CART.inp + DESTINATION ${CMAKE_CURRENT_BINARY_DIR} ) + +FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/1l2y_micro.inp + DESTINATION ${CMAKE_CURRENT_BINARY_DIR} ) + +FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Y.pdb + DESTINATION ${CMAKE_CURRENT_BINARY_DIR} ) + + FILE(COPY ${CMAKE_SOURCE_DIR}/ctest/prota_unres_energy_check.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR} FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE ) -if(NOT UNRES_WITH_MPI) - set(prota_unres_energy_output "prota_ENE.out_GB") - set(fgprocs "1") -else(NOT UNRES_WITH_MPI) - set(prota_unres_energy_output "prota_ENE.out_GB000") - set(fgprocs "2") -endif(NOT UNRES_WITH_MPI) - #========================================= # test_prota_E0LL2Y.sh #========================================= @@ -408,8 +410,8 @@ endif(NOT UNRES_WITH_MPI) FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/scripts/test_prota_E0LL2Y.sh "#!/bin/sh export POT=GB -export FGPROCS=${fgprocs} -export PREFIX=prota_ENE +export FGPROCS=$2 +export PREFIX=$1 #----------------------------------------------------------------------------- UNRES_BIN=${CMAKE_BINARY_DIR}/bin/${UNRES_BIN} #----------------------------------------------------------------------------- @@ -430,7 +432,7 @@ export PATTERN=$DD/patterns.cart #----------------------------------------------------------------------------- echo CTEST_FULL_OUTPUT $UNRES_BIN -./prota_unres_energy_check.sh ${prota_unres_energy_output} +./prota_unres_energy_check.sh $1 ${UNRES_BIN} ") # @@ -453,7 +455,9 @@ if(NOT UNRES_WITH_MPI) endif(UNRES_MD_FF STREQUAL "GAB") if(UNRES_MD_FF STREQUAL "E0LL2Y") - add_test(NAME UNRES_MD_prota COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh ) + add_test(NAME UNRES_ENE_prota COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh prota_ENE 1 ) + add_test(NAME UNRES_MIN_prota COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh prota_MIN_CART 1 ) + add_test(NAME UNRES_MD_microcanonical COMMAND sh ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh 1l2y_micro 1 ) endif(UNRES_MD_FF STREQUAL "E0LL2Y") else(NOT UNRES_WITH_MPI) @@ -463,7 +467,9 @@ else(NOT UNRES_WITH_MPI) endif(UNRES_MD_FF STREQUAL "GAB") if(UNRES_MD_FF STREQUAL "E0LL2Y") - add_test(NAME UNRES_MD_prota COMMAND mpiexec -boot -np 2 ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh ) + add_test(NAME UNRES_ENE_prota COMMAND mpiexec -boot -np 2 ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh prota_ENE 2 ) + add_test(NAME UNRES_MIN_prota COMMAND mpiexec -boot -np 2 ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh prota_MIN_CART 2 ) + add_test(NAME UNRES_MD_microcanonical COMMAND mpiexec -boot -np 2 ${CMAKE_CURRENT_BINARY_DIR}/test_prota_E0LL2Y.sh 1l2y_micro 2 ) endif(UNRES_MD_FF STREQUAL "E0LL2Y") endif(NOT UNRES_WITH_MPI)