diff --git a/regtest/basic/rt-molinfo/h.gro.reference b/regtest/basic/rt-molinfo/h.gro.reference new file mode 100644 index 0000000000000000000000000000000000000000..0c0f2906be44895e81949a247a1498c1b6b82fb5 --- /dev/null +++ b/regtest/basic/rt-molinfo/h.gro.reference @@ -0,0 +1,152 @@ +Made with PLUMED t=0.000000 +149 + 1RA5 H5T 1 4.244 3.090 1.918 + 1RA5 1H5' 4 4.447 3.058 1.901 + 1RA5 2H5' 5 4.442 3.161 2.051 + 1RA5 H4' 7 4.607 3.252 1.923 + 1RA5 H1' 10 4.581 3.395 1.622 + 1RA5 H8 13 4.267 3.230 1.687 + 1RA5 H61 18 3.924 3.551 1.479 + 1RA5 H62 19 3.956 3.710 1.424 + 1RA5 H2 22 4.388 3.795 1.426 + 1RA5 H3' 26 4.361 3.427 1.926 + 1RA5 1H2' 28 4.490 3.578 1.789 + 1RA5 2HO' 30 4.692 3.470 1.908 + 2 RG 1H5' 37 4.657 3.685 2.021 + 2 RG 2H5' 38 4.639 3.797 2.153 + 2 RG H4' 40 4.656 3.937 1.971 + 2 RG H1' 43 4.441 3.967 1.702 + 2 RG H8 46 4.280 3.705 1.918 + 2 RG H1 52 3.898 4.014 1.508 + 2 RG H21 55 3.999 4.197 1.440 + 2 RG H22 56 4.163 4.242 1.476 + 2 RG H3' 60 4.377 3.932 2.065 + 2 RG 1H2' 62 4.324 4.101 1.909 + 2 RG 2HO' 64 4.564 4.189 1.903 + 3 RC 1H5' 71 4.507 4.321 2.047 + 3 RC 2H5' 72 4.444 4.425 2.170 + 3 RC H4' 74 4.353 4.497 1.976 + 3 RC H1' 77 4.108 4.372 1.788 + 3 RC H6 80 4.138 4.123 2.063 + 3 RC H5 82 3.983 3.935 2.052 + 3 RC H41 85 3.792 3.837 1.948 + 3 RC H42 86 3.671 3.940 1.873 + 3 RC H3' 91 4.156 4.389 2.174 + 3 RC 1H2' 93 3.984 4.452 2.017 + 3 RC 2HO' 95 4.167 4.646 1.925 + 4RG3 1H5' 102 4.011 4.757 2.086 + 4RG3 2H5' 103 3.990 4.857 2.226 + 4RG3 H4' 105 3.795 4.853 2.080 + 4RG3 H1' 108 3.581 4.676 2.079 + 4RG3 H8 111 3.793 4.382 2.219 + 4RG3 H1 117 3.286 4.182 1.879 + 4RG3 H21 120 3.175 4.372 1.801 + 4RG3 H22 121 3.227 4.525 1.862 + 4RG3 H3' 125 3.793 4.800 2.357 + 4RG3 1H2' 127 3.725 4.582 2.328 + 4RG3 2HO' 129 3.516 4.575 2.391 + 4RG3 H3T 131 3.572 4.861 2.319 + 1RC5 H5T 132 2.634 3.727 1.763 + 1RC5 1H5' 135 2.466 3.850 1.706 + 1RC5 2H5' 136 2.522 3.834 1.539 + 1RC5 H4' 138 2.549 4.070 1.616 + 1RC5 H1' 141 2.813 4.198 1.779 + 1RC5 H6 144 2.820 3.836 1.799 + 1RC5 H5 146 3.014 3.727 1.889 + 1RC5 H41 149 3.242 3.780 1.998 + 1RC5 H42 150 3.325 3.917 1.969 + 1RC5 H3' 155 2.805 3.914 1.543 + 1RC5 1H2' 157 2.914 4.128 1.543 + 1RC5 2HO' 159 2.701 4.227 1.468 + 2 RG 1H5' 166 2.814 4.253 1.243 + 2 RG 2H5' 167 2.901 4.162 1.114 + 2 RG H4' 169 2.994 4.383 1.214 + 2 RG H1' 172 3.221 4.359 1.462 + 2 RG H8 175 3.112 4.001 1.420 + 2 RG H1 181 3.654 4.117 1.746 + 2 RG H21 184 3.716 4.316 1.706 + 2 RG H22 185 3.629 4.427 1.598 + 2 RG H3' 189 3.147 4.136 1.165 + 2 RG 1H2' 191 3.352 4.231 1.248 + 2 RG 2HO' 193 3.371 4.444 1.262 + 3 RC 1H5' 200 3.368 4.490 0.951 + 3 RC 2H5' 201 3.461 4.427 0.824 + 3 RC H4' 203 3.579 4.546 1.014 + 3 RC H1' 206 3.695 4.426 1.276 + 3 RC H6 209 3.508 4.149 1.112 + 3 RC H5 211 3.500 3.931 1.213 + 3 RC H41 214 3.571 3.795 1.407 + 3 RC H42 215 3.695 3.843 1.514 + 3 RC H3' 220 3.675 4.281 0.916 + 3 RC 1H2' 222 3.845 4.288 1.081 + 3 RC 2HO' 224 3.837 4.544 1.029 + 4RU3 1H5' 231 4.045 4.540 0.941 + 4RU3 2H5' 232 4.111 4.523 0.780 + 4RU3 H4' 234 4.289 4.471 0.924 + 4RU3 H1' 237 4.331 4.253 1.155 + 4RU3 H6 240 4.024 4.172 0.967 + 4RU3 H5 242 3.860 4.011 1.063 + 4RU3 H3 246 4.156 3.880 1.323 + 4RU3 H3' 250 4.163 4.214 0.820 + 4RU3 1H2' 252 4.343 4.103 0.931 + 4RU3 2HO' 254 4.496 4.267 0.866 + 4RU3 H3T 256 4.281 4.267 0.667 + 5SOL HW2 258 4.221 1.026 1.891 + 5SOL HW3 259 4.077 1.063 1.919 + 6SOL HW2 262 2.671 1.886 0.170 + 6SOL HW3 263 2.568 1.995 0.147 + 7SOL HW2 266 2.769 1.694 3.332 + 7SOL HW3 267 2.913 1.714 3.375 + 8SOL HW2 270 3.646 2.126 3.201 + 8SOL HW3 271 3.597 1.983 3.199 + 9SOL HW2 274 2.426 0.171 0.510 + 9SOL HW3 275 2.458 0.029 0.550 + 10SOL HW2 278 3.336 3.782 3.603 + 10SOL HW3 279 3.197 3.739 3.560 + 11SOL HW2 282 1.097 4.926 0.357 + 11SOL HW3 283 1.179 5.048 0.319 + 12SOL HW2 286 4.023 3.483 2.321 + 12SOL HW3 287 4.140 3.480 2.417 + 13SOL HW2 290 3.411 3.941 0.061 + 13SOL HW3 291 3.290 3.970 -0.026 + 14SOL HW2 294 5.779 1.498 3.193 + 14SOL HW3 295 5.903 1.575 3.154 + 15SOL HW2 298 4.077 0.333 0.635 + 15SOL HW3 299 4.160 0.239 0.720 + 16SOL HW2 302 1.758 4.200 0.573 + 16SOL HW3 303 1.607 4.197 0.585 + 17SOL HW2 306 4.022 1.932 1.058 + 17SOL HW3 307 4.084 1.822 0.974 + 18SOL HW2 310 1.051 4.827 0.869 + 18SOL HW3 311 0.978 4.954 0.830 + 19SOL HW2 314 3.819 3.141 0.592 + 19SOL HW3 315 3.710 3.056 0.531 + 20SOL HW2 318 5.532 2.279 3.072 + 20SOL HW3 319 5.483 2.370 2.962 + 21SOL HW2 322 3.413 1.434 2.620 + 21SOL HW3 323 3.265 1.405 2.634 + 22SOL HW2 326 5.090 0.957 1.066 + 22SOL HW3 327 5.242 0.963 1.067 + 23SOL HW2 330 1.536 5.014 0.217 + 23SOL HW3 331 1.645 4.954 0.304 + 24SOL HW2 334 3.360 0.368 1.166 + 24SOL HW3 335 3.432 0.270 1.077 + 25SOL HW2 338 2.362 3.208 1.361 + 25SOL HW3 339 2.329 3.238 1.216 + 26SOL HW2 342 6.846 4.662 3.030 + 26SOL HW3 343 6.768 4.557 3.106 + 27SOL HW2 346 5.589 2.613 2.970 + 27SOL HW3 347 5.663 2.599 2.839 + 28SOL HW2 350 1.380 4.689 0.122 + 28SOL HW3 351 1.271 4.584 0.134 + 29SOL HW2 354 5.222 1.421 1.137 + 29SOL HW3 355 5.159 1.552 1.179 + 30SOL HW2 358 4.543 4.963 1.060 + 30SOL HW3 359 4.667 4.906 0.995 + 31SOL HW2 362 4.166 3.206 2.815 + 31SOL HW3 363 4.316 3.183 2.820 + 32SOL HW2 366 6.397 1.562 3.506 + 32SOL HW3 367 6.393 1.420 3.455 + 33SOL HW2 370 2.230 1.668 1.730 + 33SOL HW3 371 2.165 1.532 1.716 + 5.1638000 5.1638000 3.6513500 0.0000000 0.0000000 0.0000000 0.0000000 2.5819000 2.5819000 diff --git a/regtest/basic/rt-molinfo/nh.gro.reference b/regtest/basic/rt-molinfo/nh.gro.reference new file mode 100644 index 0000000000000000000000000000000000000000..2de04c3bf6dc39aafc48fb25526701bcc4e227d0 --- /dev/null +++ b/regtest/basic/rt-molinfo/nh.gro.reference @@ -0,0 +1,244 @@ +Made with PLUMED t=0.000000 +241 + 1RA5 O5' 2 4.284 3.177 1.930 + 1RA5 C5' 3 4.423 3.155 1.944 + 1RA5 C4' 6 4.507 3.266 1.882 + 1RA5 O4' 8 4.509 3.257 1.742 + 1RA5 C1' 9 4.493 3.385 1.685 + 1RA5 N9 11 4.355 3.414 1.644 + 1RA5 C8 12 4.248 3.329 1.648 + 1RA5 N7 14 4.139 3.381 1.599 + 1RA5 C5 15 4.180 3.504 1.548 + 1RA5 C6 16 4.122 3.613 1.480 + 1RA5 N6 17 3.992 3.619 1.449 + 1RA5 N1 20 4.191 3.718 1.435 + 1RA5 C2 21 4.320 3.720 1.464 + 1RA5 N3 23 4.386 3.632 1.537 + 1RA5 C4 24 4.314 3.522 1.569 + 1RA5 C3' 25 4.469 3.408 1.923 + 1RA5 C2' 27 4.530 3.477 1.801 + 1RA5 O2' 29 4.670 3.472 1.815 + 1RA5 O3' 31 4.535 3.444 2.042 + 2 RG P 32 4.475 3.539 2.157 + 2 RG O1P 33 4.581 3.541 2.260 + 2 RG O2P 34 4.338 3.491 2.189 + 2 RG O5' 35 4.472 3.688 2.097 + 2 RG C5' 36 4.589 3.759 2.063 + 2 RG C4' 39 4.566 3.876 1.968 + 2 RG O4' 41 4.519 3.839 1.840 + 2 RG C1' 42 4.422 3.935 1.804 + 2 RG N9 44 4.285 3.882 1.794 + 2 RG C8 45 4.226 3.776 1.857 + 2 RG N7 47 4.107 3.746 1.814 + 2 RG C5 48 4.084 3.843 1.717 + 2 RG C6 49 3.968 3.876 1.643 + 2 RG O6 50 3.856 3.826 1.638 + 2 RG N1 51 3.981 3.986 1.559 + 2 RG C2 53 4.095 4.063 1.556 + 2 RG N2 54 4.089 4.175 1.482 + 2 RG N3 57 4.205 4.039 1.628 + 2 RG C4 58 4.192 3.927 1.704 + 2 RG C3' 59 4.465 3.978 2.020 + 2 RG C2' 61 4.423 4.057 1.896 + 2 RG O2' 63 4.524 4.135 1.835 + 2 RG O3' 65 4.533 4.066 2.107 + 3 RC P 66 4.456 4.124 2.235 + 3 RC O1P 67 4.559 4.194 2.315 + 3 RC O2P 68 4.364 4.030 2.304 + 3 RC O5' 69 4.362 4.236 2.168 + 3 RC C5' 70 4.415 4.347 2.100 + 3 RC C4' 73 4.305 4.405 2.010 + 3 RC O4' 75 4.248 4.312 1.921 + 3 RC C1' 76 4.115 4.348 1.894 + 3 RC N1 78 4.020 4.239 1.925 + 3 RC C6 79 4.048 4.130 2.003 + 3 RC C5 81 3.962 4.027 1.999 + 3 RC C4 83 3.843 4.033 1.919 + 3 RC N4 84 3.759 3.929 1.921 + 3 RC N3 87 3.816 4.140 1.843 + 3 RC C2 88 3.903 4.244 1.851 + 3 RC O2 89 3.877 4.343 1.783 + 3 RC C3' 90 4.187 4.455 2.093 + 3 RC C2' 92 4.085 4.470 1.980 + 3 RC O2' 94 4.098 4.585 1.899 + 3 RC O3' 96 4.215 4.583 2.144 + 4RG3 P 97 4.155 4.634 2.285 + 4RG3 O1P 98 4.223 4.763 2.306 + 4RG3 O2P 99 4.173 4.522 2.381 + 4RG3 O5' 100 3.996 4.656 2.269 + 4RG3 C5' 101 3.961 4.762 2.182 + 4RG3 C4' 104 3.814 4.767 2.143 + 4RG3 O4' 106 3.779 4.646 2.079 + 4RG3 C1' 107 3.652 4.611 2.130 + 4RG3 N9 109 3.625 4.467 2.114 + 4RG3 C8 110 3.703 4.364 2.161 + 4RG3 N7 112 3.663 4.244 2.131 + 4RG3 C5 113 3.552 4.265 2.050 + 4RG3 C6 114 3.457 4.172 1.999 + 4RG3 O6 115 3.457 4.050 2.000 + 4RG3 N1 116 3.357 4.236 1.927 + 4RG3 C2 118 3.343 4.373 1.926 + 4RG3 N2 119 3.244 4.425 1.852 + 4RG3 N3 122 3.418 4.460 1.994 + 4RG3 C4 123 3.524 4.399 2.050 + 4RG3 C3' 124 3.730 4.784 2.270 + 4RG3 C2' 126 3.657 4.651 2.278 + 4RG3 O2' 128 3.531 4.656 2.342 + 4RG3 O3' 130 3.637 4.890 2.255 + 1RC5 O5' 133 2.636 3.747 1.669 + 1RC5 C5' 134 2.553 3.857 1.641 + 1RC5 C4' 137 2.622 3.993 1.640 + 1RC5 O4' 139 2.675 4.045 1.760 + 1RC5 C1' 140 2.802 4.099 1.733 + 1RC5 N1 142 2.920 4.024 1.779 + 1RC5 C6 143 2.911 3.891 1.812 + 1RC5 C5 145 3.023 3.830 1.857 + 1RC5 C4 147 3.138 3.912 1.878 + 1RC5 N4 148 3.247 3.861 1.938 + 1RC5 N3 151 3.147 4.041 1.844 + 1RC5 C2 152 3.034 4.100 1.795 + 1RC5 O2 153 3.051 4.219 1.770 + 1RC5 C3' 154 2.735 3.997 1.537 + 1RC5 C2' 156 2.813 4.120 1.582 + 1RC5 O2' 158 2.747 4.241 1.551 + 1RC5 O3' 160 2.681 4.015 1.408 + 2 RG P 161 2.764 3.967 1.279 + 2 RG O1P 162 2.683 4.010 1.163 + 2 RG O2P 163 2.805 3.826 1.297 + 2 RG O5' 164 2.889 4.067 1.292 + 2 RG C5' 165 2.898 4.188 1.219 + 2 RG C4' 168 3.018 4.280 1.244 + 2 RG O4' 170 3.054 4.277 1.380 + 2 RG C1' 171 3.194 4.278 1.393 + 2 RG N9 173 3.245 4.158 1.461 + 2 RG C8 174 3.203 4.028 1.471 + 2 RG N7 176 3.276 3.950 1.546 + 2 RG C5 177 3.382 4.031 1.584 + 2 RG C6 178 3.491 4.012 1.673 + 2 RG O6 179 3.523 3.911 1.734 + 2 RG N1 180 3.571 4.125 1.690 + 2 RG C2 182 3.539 4.248 1.636 + 2 RG N2 183 3.637 4.339 1.648 + 2 RG N3 186 3.434 4.269 1.556 + 2 RG C4 187 3.363 4.156 1.532 + 2 RG C3' 188 3.146 4.245 1.168 + 2 RG C2' 190 3.261 4.291 1.256 + 2 RG O2' 192 3.281 4.428 1.230 + 2 RG O3' 194 3.141 4.299 1.038 + 3 RC P 195 3.237 4.241 0.922 + 3 RC O1P 196 3.197 4.314 0.800 + 3 RC O2P 197 3.233 4.093 0.938 + 3 RC O5' 198 3.388 4.283 0.956 + 3 RC C5' 199 3.441 4.411 0.930 + 3 RC C4' 202 3.566 4.437 1.012 + 3 RC O4' 204 3.547 4.388 1.143 + 3 RC C1' 205 3.675 4.358 1.193 + 3 RC N1 207 3.668 4.218 1.238 + 3 RC C6 208 3.582 4.125 1.188 + 3 RC C5 210 3.577 4.001 1.241 + 3 RC C4 212 3.657 3.972 1.356 + 3 RC N4 213 3.642 3.862 1.431 + 3 RC N3 216 3.749 4.061 1.398 + 3 RC C2 217 3.758 4.182 1.337 + 3 RC O2 218 3.837 4.261 1.389 + 3 RC C3' 219 3.695 4.382 0.951 + 3 RC C2' 221 3.777 4.373 1.080 + 3 RC O2' 223 3.848 4.491 1.108 + 3 RC O3' 225 3.753 4.470 0.858 + 4RU3 P 226 3.857 4.421 0.744 + 4RU3 O1P 227 3.886 4.541 0.663 + 4RU3 O2P 228 3.807 4.301 0.674 + 4RU3 O5' 229 3.985 4.375 0.830 + 4RU3 C5' 230 4.084 4.467 0.870 + 4RU3 C4' 233 4.206 4.401 0.932 + 4RU3 O4' 235 4.184 4.357 1.065 + 4RU3 C1' 236 4.260 4.239 1.075 + 4RU3 N1 238 4.174 4.122 1.103 + 4RU3 C6 239 4.050 4.105 1.048 + 4RU3 C5 241 3.961 4.019 1.100 + 4RU3 C4 243 3.997 3.924 1.202 + 4RU3 O4 244 3.924 3.838 1.251 + 4RU3 N3 245 4.127 3.942 1.249 + 4RU3 C2 247 4.214 4.042 1.208 + 4RU3 O2 248 4.328 4.043 1.254 + 4RU3 C3' 249 4.246 4.279 0.849 + 4RU3 C2' 251 4.340 4.210 0.948 + 4RU3 O2' 253 4.472 4.258 0.958 + 4RU3 O3' 255 4.325 4.314 0.738 + 5SOL OW 257 4.162 1.101 1.896 + 5SOL MW4 260 4.162 1.101 1.896 + 6SOL OW 261 2.661 1.981 0.167 + 6SOL MW4 264 2.661 1.981 0.167 + 7SOL OW 265 2.827 1.758 3.373 + 7SOL MW4 268 2.827 1.758 3.373 + 8SOL OW 269 3.674 2.036 3.220 + 8SOL MW4 272 3.674 2.036 3.220 + 9SOL OW 273 2.398 0.101 0.569 + 9SOL MW4 276 2.398 0.101 0.569 + 10SOL OW 277 3.266 3.721 3.625 + 10SOL MW4 280 3.266 3.721 3.625 + 11SOL OW 281 1.089 5.019 0.333 + 11SOL MW4 284 1.089 5.019 0.333 + 12SOL OW 285 4.056 3.437 2.398 + 12SOL MW4 288 4.056 3.437 2.398 + 13SOL OW 289 3.318 3.921 0.051 + 13SOL MW4 292 3.318 3.921 0.051 + 14SOL OW 293 5.842 1.508 3.122 + 14SOL MW4 296 5.842 1.508 3.122 + 15SOL OW 297 4.099 0.240 0.647 + 15SOL MW4 300 4.099 0.240 0.647 + 16SOL OW 301 1.683 4.252 0.604 + 16SOL MW4 304 1.683 4.252 0.604 + 17SOL OW 305 4.025 1.837 1.048 + 17SOL MW4 308 4.025 1.837 1.048 + 18SOL OW 309 1.037 4.918 0.896 + 18SOL MW4 312 1.037 4.918 0.896 + 19SOL OW 313 3.750 3.079 0.615 + 19SOL MW4 316 3.750 3.079 0.615 + 20SOL OW 317 5.473 2.352 3.056 + 20SOL MW4 320 5.473 2.352 3.056 + 21SOL OW 321 3.327 1.472 2.603 + 21SOL MW4 324 3.327 1.472 2.603 + 22SOL OW 325 5.165 0.979 1.122 + 22SOL MW4 328 5.165 0.979 1.122 + 23SOL OW 329 1.631 5.010 0.227 + 23SOL MW4 332 1.631 5.010 0.227 + 24SOL OW 333 3.388 0.355 1.076 + 24SOL MW4 336 3.388 0.355 1.076 + 25SOL OW 337 2.397 3.250 1.282 + 25SOL MW4 340 2.397 3.250 1.282 + 26SOL OW 341 6.770 4.605 3.023 + 26SOL MW4 344 6.770 4.605 3.023 + 27SOL OW 345 5.661 2.565 2.929 + 27SOL MW4 348 5.661 2.565 2.929 + 28SOL OW 349 1.302 4.655 0.077 + 28SOL MW4 352 1.302 4.655 0.077 + 29SOL OW 353 5.202 1.509 1.105 + 29SOL MW4 356 5.202 1.509 1.105 + 30SOL OW 357 4.606 4.891 1.067 + 30SOL MW4 360 4.606 4.891 1.067 + 31SOL OW 361 4.232 3.142 2.842 + 31SOL MW4 364 4.232 3.142 2.842 + 32SOL OW 365 6.453 1.493 3.470 + 32SOL MW4 368 6.453 1.493 3.470 + 33SOL OW 369 2.243 1.580 1.692 + 33SOL MW4 372 2.243 1.580 1.692 + 3097 NA NA 373 4.161 2.915 2.814 + 3098 NA NA 374 5.871 1.736 2.620 + 3099 NA NA 375 6.217 2.138 2.137 + 3100 NA NA 376 2.842 1.094 2.561 + 3101 NA NA 377 3.488 4.969 0.147 + 3102 NA NA 378 2.922 3.381 1.088 + 3103 NA NA 379 2.666 1.091 3.617 + 3104 NA NA 380 2.799 0.031 2.321 + 3105 NA NA 381 5.153 0.373 1.826 + 3106 NA NA 382 6.016 3.193 2.648 + 3107 NA NA 383 2.061 5.096 1.718 + 3108 NA NA 384 5.509 2.569 1.721 + 3109 CL CL 385 4.322 4.124 0.361 + 3110 CL CL 386 6.417 1.888 3.321 + 3111 CL CL 387 2.664 0.227 1.271 + 3112 CL CL 388 1.066 4.151 0.684 + 3113 CL CL 389 2.126 2.069 1.628 + 3114 CL CL 390 4.254 0.718 2.556 + 5.1638000 5.1638000 3.6513500 0.0000000 0.0000000 0.0000000 0.0000000 2.5819000 2.5819000 diff --git a/regtest/basic/rt-molinfo/plumed.dat b/regtest/basic/rt-molinfo/plumed.dat index 82851c67cbfce81d4df6a25846c83bb72aa67d64..f1ec224d10173fa1c8393a9e094f25fd2a2ec836 100644 --- a/regtest/basic/rt-molinfo/plumed.dat +++ b/regtest/basic/rt-molinfo/plumed.dat @@ -4,3 +4,5 @@ DUMPATOMS ATOMS=@water FILE=water.gro DUMPATOMS ATOMS=@ions FILE=ions.gro # notice that here water is labeled as chain C: DUMPATOMS ATOMS=@OW-C8 FILE=oneox.gro +DUMPATOMS ATOMS=@hydrogens FILE=h.gro +DUMPATOMS ATOMS=@nonhydrogens FILE=nh.gro