diff --git a/.travis/push b/.travis/push
index 98b4c15ba565c7c26cd455c820ecc023d5688df0..e13da62a87851abb68bd3bcb9531673190321a78 100755
--- a/.travis/push
+++ b/.travis/push
@@ -15,6 +15,11 @@ set -x
GIT_OWNER=$( echo $TRAVIS_REPO_SLUG | sed "s/\/.*$//" )
GIT_REPO=$( echo $TRAVIS_REPO_SLUG | sed "s/^.*\///" )
+if [ "$TRAVIS_PULL_REQUEST" != false ] ; then
+ echo "Building from a pull request, nothing to push"
+ exit 0
+fi
+
if [ "$GIT_OWNER" = plumed ] ; then
if [[ "$TRAVIS_BRANCH" =~ ^v2\.[0-9]+$ ]] ; then
if test -f CHANGES/"$TRAVIS_BRANCH".md && grep -q plumednotmaintained CHANGES/"$TRAVIS_BRANCH".md ; then
diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md
index cda9155c7c07bc1889b8e4185476d192e300cc3b..b47969a44664717a7f634e5a3a82ea0805ddc4f1 100644
--- a/CHANGES/v2.5.md
+++ b/CHANGES/v2.5.md
@@ -47,6 +47,9 @@ Changes from version 2.4 which are relevant for users:
- \ref RMSD calculation has been optimized. This should positively affect the performances of CVs where
many RMSDs are computed on small groups of atoms, such as secondary structure variables.
- In \ref METAD, when using a bias factor equal to one (no bias) the `rct` component is set to zero rather than to one.
+ - New shortcuts are available for selecting atoms: `@allatoms` and `@mdatoms` (see \ref atomSpecs).
+ - When using \ref MOLINFO, also the following shortcuts are available for selecting atoms: `@nucleic`, `@protein`, `@water`, `@ions`, `@hydrogens`, `@nonhydrogens`.
+ - When using \ref MOLINFO, individual atoms can be chosen also from water molecules (e.g. `@OW-100`).
Changes from version 2.4 which are relevant for developers:
- Code has been cleanup up replacing a number of pointers with `std::unique_ptr`. All `delete` statements
diff --git a/regtest/basic/rt-molinfo/Makefile b/regtest/basic/rt-molinfo/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-molinfo/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-molinfo/config b/regtest/basic/rt-molinfo/config
new file mode 100644
index 0000000000000000000000000000000000000000..8aa5237159454be6d5df63ab4078ee04a7a61dc0
--- /dev/null
+++ b/regtest/basic/rt-molinfo/config
@@ -0,0 +1,2 @@
+type=driver
+arg="--igro test.gro --plumed plumed.dat"
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/ions.gro.reference b/regtest/basic/rt-molinfo/ions.gro.reference
new file mode 100644
index 0000000000000000000000000000000000000000..892eb2592f2270c7046730bfd5e48ed1e26361ce
--- /dev/null
+++ b/regtest/basic/rt-molinfo/ions.gro.reference
@@ -0,0 +1,21 @@
+Made with PLUMED t=0.000000
+18
+ 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/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/nucleic.gro.reference b/regtest/basic/rt-molinfo/nucleic.gro.reference
new file mode 100644
index 0000000000000000000000000000000000000000..dd685c57761badac3613e6e2bd35d6eea2e017a9
--- /dev/null
+++ b/regtest/basic/rt-molinfo/nucleic.gro.reference
@@ -0,0 +1,259 @@
+Made with PLUMED t=0.000000
+256
+ 1RA5 H5T 1 4.244 3.090 1.918
+ 1RA5 O5' 2 4.284 3.177 1.930
+ 1RA5 C5' 3 4.423 3.155 1.944
+ 1RA5 1H5' 4 4.447 3.058 1.901
+ 1RA5 2H5' 5 4.442 3.161 2.051
+ 1RA5 C4' 6 4.507 3.266 1.882
+ 1RA5 H4' 7 4.607 3.252 1.923
+ 1RA5 O4' 8 4.509 3.257 1.742
+ 1RA5 C1' 9 4.493 3.385 1.685
+ 1RA5 H1' 10 4.581 3.395 1.622
+ 1RA5 N9 11 4.355 3.414 1.644
+ 1RA5 C8 12 4.248 3.329 1.648
+ 1RA5 H8 13 4.267 3.230 1.687
+ 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 H61 18 3.924 3.551 1.479
+ 1RA5 H62 19 3.956 3.710 1.424
+ 1RA5 N1 20 4.191 3.718 1.435
+ 1RA5 C2 21 4.320 3.720 1.464
+ 1RA5 H2 22 4.388 3.795 1.426
+ 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 H3' 26 4.361 3.427 1.926
+ 1RA5 C2' 27 4.530 3.477 1.801
+ 1RA5 1H2' 28 4.490 3.578 1.789
+ 1RA5 O2' 29 4.670 3.472 1.815
+ 1RA5 2HO' 30 4.692 3.470 1.908
+ 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 1H5' 37 4.657 3.685 2.021
+ 2 RG 2H5' 38 4.639 3.797 2.153
+ 2 RG C4' 39 4.566 3.876 1.968
+ 2 RG H4' 40 4.656 3.937 1.971
+ 2 RG O4' 41 4.519 3.839 1.840
+ 2 RG C1' 42 4.422 3.935 1.804
+ 2 RG H1' 43 4.441 3.967 1.702
+ 2 RG N9 44 4.285 3.882 1.794
+ 2 RG C8 45 4.226 3.776 1.857
+ 2 RG H8 46 4.280 3.705 1.918
+ 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 H1 52 3.898 4.014 1.508
+ 2 RG C2 53 4.095 4.063 1.556
+ 2 RG N2 54 4.089 4.175 1.482
+ 2 RG H21 55 3.999 4.197 1.440
+ 2 RG H22 56 4.163 4.242 1.476
+ 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 H3' 60 4.377 3.932 2.065
+ 2 RG C2' 61 4.423 4.057 1.896
+ 2 RG 1H2' 62 4.324 4.101 1.909
+ 2 RG O2' 63 4.524 4.135 1.835
+ 2 RG 2HO' 64 4.564 4.189 1.903
+ 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 1H5' 71 4.507 4.321 2.047
+ 3 RC 2H5' 72 4.444 4.425 2.170
+ 3 RC C4' 73 4.305 4.405 2.010
+ 3 RC H4' 74 4.353 4.497 1.976
+ 3 RC O4' 75 4.248 4.312 1.921
+ 3 RC C1' 76 4.115 4.348 1.894
+ 3 RC H1' 77 4.108 4.372 1.788
+ 3 RC N1 78 4.020 4.239 1.925
+ 3 RC C6 79 4.048 4.130 2.003
+ 3 RC H6 80 4.138 4.123 2.063
+ 3 RC C5 81 3.962 4.027 1.999
+ 3 RC H5 82 3.983 3.935 2.052
+ 3 RC C4 83 3.843 4.033 1.919
+ 3 RC N4 84 3.759 3.929 1.921
+ 3 RC H41 85 3.792 3.837 1.948
+ 3 RC H42 86 3.671 3.940 1.873
+ 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 H3' 91 4.156 4.389 2.174
+ 3 RC C2' 92 4.085 4.470 1.980
+ 3 RC 1H2' 93 3.984 4.452 2.017
+ 3 RC O2' 94 4.098 4.585 1.899
+ 3 RC 2HO' 95 4.167 4.646 1.925
+ 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 1H5' 102 4.011 4.757 2.086
+ 4RG3 2H5' 103 3.990 4.857 2.226
+ 4RG3 C4' 104 3.814 4.767 2.143
+ 4RG3 H4' 105 3.795 4.853 2.080
+ 4RG3 O4' 106 3.779 4.646 2.079
+ 4RG3 C1' 107 3.652 4.611 2.130
+ 4RG3 H1' 108 3.581 4.676 2.079
+ 4RG3 N9 109 3.625 4.467 2.114
+ 4RG3 C8 110 3.703 4.364 2.161
+ 4RG3 H8 111 3.793 4.382 2.219
+ 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 H1 117 3.286 4.182 1.879
+ 4RG3 C2 118 3.343 4.373 1.926
+ 4RG3 N2 119 3.244 4.425 1.852
+ 4RG3 H21 120 3.175 4.372 1.801
+ 4RG3 H22 121 3.227 4.525 1.862
+ 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 H3' 125 3.793 4.800 2.357
+ 4RG3 C2' 126 3.657 4.651 2.278
+ 4RG3 1H2' 127 3.725 4.582 2.328
+ 4RG3 O2' 128 3.531 4.656 2.342
+ 4RG3 2HO' 129 3.516 4.575 2.391
+ 4RG3 O3' 130 3.637 4.890 2.255
+ 4RG3 H3T 131 3.572 4.861 2.319
+ 1RC5 H5T 132 2.634 3.727 1.763
+ 1RC5 O5' 133 2.636 3.747 1.669
+ 1RC5 C5' 134 2.553 3.857 1.641
+ 1RC5 1H5' 135 2.466 3.850 1.706
+ 1RC5 2H5' 136 2.522 3.834 1.539
+ 1RC5 C4' 137 2.622 3.993 1.640
+ 1RC5 H4' 138 2.549 4.070 1.616
+ 1RC5 O4' 139 2.675 4.045 1.760
+ 1RC5 C1' 140 2.802 4.099 1.733
+ 1RC5 H1' 141 2.813 4.198 1.779
+ 1RC5 N1 142 2.920 4.024 1.779
+ 1RC5 C6 143 2.911 3.891 1.812
+ 1RC5 H6 144 2.820 3.836 1.799
+ 1RC5 C5 145 3.023 3.830 1.857
+ 1RC5 H5 146 3.014 3.727 1.889
+ 1RC5 C4 147 3.138 3.912 1.878
+ 1RC5 N4 148 3.247 3.861 1.938
+ 1RC5 H41 149 3.242 3.780 1.998
+ 1RC5 H42 150 3.325 3.917 1.969
+ 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 H3' 155 2.805 3.914 1.543
+ 1RC5 C2' 156 2.813 4.120 1.582
+ 1RC5 1H2' 157 2.914 4.128 1.543
+ 1RC5 O2' 158 2.747 4.241 1.551
+ 1RC5 2HO' 159 2.701 4.227 1.468
+ 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 1H5' 166 2.814 4.253 1.243
+ 2 RG 2H5' 167 2.901 4.162 1.114
+ 2 RG C4' 168 3.018 4.280 1.244
+ 2 RG H4' 169 2.994 4.383 1.214
+ 2 RG O4' 170 3.054 4.277 1.380
+ 2 RG C1' 171 3.194 4.278 1.393
+ 2 RG H1' 172 3.221 4.359 1.462
+ 2 RG N9 173 3.245 4.158 1.461
+ 2 RG C8 174 3.203 4.028 1.471
+ 2 RG H8 175 3.112 4.001 1.420
+ 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 H1 181 3.654 4.117 1.746
+ 2 RG C2 182 3.539 4.248 1.636
+ 2 RG N2 183 3.637 4.339 1.648
+ 2 RG H21 184 3.716 4.316 1.706
+ 2 RG H22 185 3.629 4.427 1.598
+ 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 H3' 189 3.147 4.136 1.165
+ 2 RG C2' 190 3.261 4.291 1.256
+ 2 RG 1H2' 191 3.352 4.231 1.248
+ 2 RG O2' 192 3.281 4.428 1.230
+ 2 RG 2HO' 193 3.371 4.444 1.262
+ 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 1H5' 200 3.368 4.490 0.951
+ 3 RC 2H5' 201 3.461 4.427 0.824
+ 3 RC C4' 202 3.566 4.437 1.012
+ 3 RC H4' 203 3.579 4.546 1.014
+ 3 RC O4' 204 3.547 4.388 1.143
+ 3 RC C1' 205 3.675 4.358 1.193
+ 3 RC H1' 206 3.695 4.426 1.276
+ 3 RC N1 207 3.668 4.218 1.238
+ 3 RC C6 208 3.582 4.125 1.188
+ 3 RC H6 209 3.508 4.149 1.112
+ 3 RC C5 210 3.577 4.001 1.241
+ 3 RC H5 211 3.500 3.931 1.213
+ 3 RC C4 212 3.657 3.972 1.356
+ 3 RC N4 213 3.642 3.862 1.431
+ 3 RC H41 214 3.571 3.795 1.407
+ 3 RC H42 215 3.695 3.843 1.514
+ 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 H3' 220 3.675 4.281 0.916
+ 3 RC C2' 221 3.777 4.373 1.080
+ 3 RC 1H2' 222 3.845 4.288 1.081
+ 3 RC O2' 223 3.848 4.491 1.108
+ 3 RC 2HO' 224 3.837 4.544 1.029
+ 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 1H5' 231 4.045 4.540 0.941
+ 4RU3 2H5' 232 4.111 4.523 0.780
+ 4RU3 C4' 233 4.206 4.401 0.932
+ 4RU3 H4' 234 4.289 4.471 0.924
+ 4RU3 O4' 235 4.184 4.357 1.065
+ 4RU3 C1' 236 4.260 4.239 1.075
+ 4RU3 H1' 237 4.331 4.253 1.155
+ 4RU3 N1 238 4.174 4.122 1.103
+ 4RU3 C6 239 4.050 4.105 1.048
+ 4RU3 H6 240 4.024 4.172 0.967
+ 4RU3 C5 241 3.961 4.019 1.100
+ 4RU3 H5 242 3.860 4.011 1.063
+ 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 H3 246 4.156 3.880 1.323
+ 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 H3' 250 4.163 4.214 0.820
+ 4RU3 C2' 251 4.340 4.210 0.948
+ 4RU3 1H2' 252 4.343 4.103 0.931
+ 4RU3 O2' 253 4.472 4.258 0.958
+ 4RU3 2HO' 254 4.496 4.267 0.866
+ 4RU3 O3' 255 4.325 4.314 0.738
+ 4RU3 H3T 256 4.281 4.267 0.667
+ 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/oneox.gro.reference b/regtest/basic/rt-molinfo/oneox.gro.reference
new file mode 100644
index 0000000000000000000000000000000000000000..e5b636d622857579f20f16e24ec557f7e30aae20
--- /dev/null
+++ b/regtest/basic/rt-molinfo/oneox.gro.reference
@@ -0,0 +1,4 @@
+Made with PLUMED t=0.000000
+1
+ 8SOL OW 269 3.674 2.036 3.220
+ 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
new file mode 100644
index 0000000000000000000000000000000000000000..f1ec224d10173fa1c8393a9e094f25fd2a2ec836
--- /dev/null
+++ b/regtest/basic/rt-molinfo/plumed.dat
@@ -0,0 +1,8 @@
+MOLINFO STRUCTURE=test.pdb
+DUMPATOMS ATOMS=@nucleic FILE=nucleic.gro
+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
diff --git a/regtest/basic/rt-molinfo/test.gro b/regtest/basic/rt-molinfo/test.gro
new file mode 100644
index 0000000000000000000000000000000000000000..2e507727f748f9d6a2c161c959d2b7772a0aef20
--- /dev/null
+++ b/regtest/basic/rt-molinfo/test.gro
@@ -0,0 +1,393 @@
+Protein in water
+390
+ 1RA5 H5T 1 4.244 3.090 1.918
+ 1RA5 O5' 2 4.284 3.177 1.930
+ 1RA5 C5' 3 4.423 3.155 1.944
+ 1RA5 H5'1 4 4.447 3.058 1.901
+ 1RA5 H5'2 5 4.442 3.161 2.051
+ 1RA5 C4' 6 4.507 3.266 1.882
+ 1RA5 H4' 7 4.607 3.252 1.923
+ 1RA5 O4' 8 4.509 3.257 1.742
+ 1RA5 C1' 9 4.493 3.385 1.685
+ 1RA5 H1' 10 4.581 3.395 1.622
+ 1RA5 N9 11 4.355 3.414 1.644
+ 1RA5 C8 12 4.248 3.329 1.648
+ 1RA5 H8 13 4.267 3.230 1.687
+ 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 H61 18 3.924 3.551 1.479
+ 1RA5 H62 19 3.956 3.710 1.424
+ 1RA5 N1 20 4.191 3.718 1.435
+ 1RA5 C2 21 4.320 3.720 1.464
+ 1RA5 H2 22 4.388 3.795 1.426
+ 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 H3' 26 4.361 3.427 1.926
+ 1RA5 C2' 27 4.530 3.477 1.801
+ 1RA5 H2'1 28 4.490 3.578 1.789
+ 1RA5 O2' 29 4.670 3.472 1.815
+ 1RA5 HO'2 30 4.692 3.470 1.908
+ 1RA5 O3' 31 4.535 3.444 2.042
+ 2RG P 32 4.475 3.539 2.157
+ 2RG O1P 33 4.581 3.541 2.260
+ 2RG O2P 34 4.338 3.491 2.189
+ 2RG O5' 35 4.472 3.688 2.097
+ 2RG C5' 36 4.589 3.759 2.063
+ 2RG H5'1 37 4.657 3.685 2.021
+ 2RG H5'2 38 4.639 3.797 2.153
+ 2RG C4' 39 4.566 3.876 1.968
+ 2RG H4' 40 4.656 3.937 1.971
+ 2RG O4' 41 4.519 3.839 1.840
+ 2RG C1' 42 4.422 3.935 1.804
+ 2RG H1' 43 4.441 3.967 1.702
+ 2RG N9 44 4.285 3.882 1.794
+ 2RG C8 45 4.226 3.776 1.857
+ 2RG H8 46 4.280 3.705 1.918
+ 2RG N7 47 4.107 3.746 1.814
+ 2RG C5 48 4.084 3.843 1.717
+ 2RG C6 49 3.968 3.876 1.643
+ 2RG O6 50 3.856 3.826 1.638
+ 2RG N1 51 3.981 3.986 1.559
+ 2RG H1 52 3.898 4.014 1.508
+ 2RG C2 53 4.095 4.063 1.556
+ 2RG N2 54 4.089 4.175 1.482
+ 2RG H21 55 3.999 4.197 1.440
+ 2RG H22 56 4.163 4.242 1.476
+ 2RG N3 57 4.205 4.039 1.628
+ 2RG C4 58 4.192 3.927 1.704
+ 2RG C3' 59 4.465 3.978 2.020
+ 2RG H3' 60 4.377 3.932 2.065
+ 2RG C2' 61 4.423 4.057 1.896
+ 2RG H2'1 62 4.324 4.101 1.909
+ 2RG O2' 63 4.524 4.135 1.835
+ 2RG HO'2 64 4.564 4.189 1.903
+ 2RG O3' 65 4.533 4.066 2.107
+ 3RC P 66 4.456 4.124 2.235
+ 3RC O1P 67 4.559 4.194 2.315
+ 3RC O2P 68 4.364 4.030 2.304
+ 3RC O5' 69 4.362 4.236 2.168
+ 3RC C5' 70 4.415 4.347 2.100
+ 3RC H5'1 71 4.507 4.321 2.047
+ 3RC H5'2 72 4.444 4.425 2.170
+ 3RC C4' 73 4.305 4.405 2.010
+ 3RC H4' 74 4.353 4.497 1.976
+ 3RC O4' 75 4.248 4.312 1.921
+ 3RC C1' 76 4.115 4.348 1.894
+ 3RC H1' 77 4.108 4.372 1.788
+ 3RC N1 78 4.020 4.239 1.925
+ 3RC C6 79 4.048 4.130 2.003
+ 3RC H6 80 4.138 4.123 2.063
+ 3RC C5 81 3.962 4.027 1.999
+ 3RC H5 82 3.983 3.935 2.052
+ 3RC C4 83 3.843 4.033 1.919
+ 3RC N4 84 3.759 3.929 1.921
+ 3RC H41 85 3.792 3.837 1.948
+ 3RC H42 86 3.671 3.940 1.873
+ 3RC N3 87 3.816 4.140 1.843
+ 3RC C2 88 3.903 4.244 1.851
+ 3RC O2 89 3.877 4.343 1.783
+ 3RC C3' 90 4.187 4.455 2.093
+ 3RC H3' 91 4.156 4.389 2.174
+ 3RC C2' 92 4.085 4.470 1.980
+ 3RC H2'1 93 3.984 4.452 2.017
+ 3RC O2' 94 4.098 4.585 1.899
+ 3RC HO'2 95 4.167 4.646 1.925
+ 3RC 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 H5'1 102 4.011 4.757 2.086
+ 4RG3 H5'2 103 3.990 4.857 2.226
+ 4RG3 C4' 104 3.814 4.767 2.143
+ 4RG3 H4' 105 3.795 4.853 2.080
+ 4RG3 O4' 106 3.779 4.646 2.079
+ 4RG3 C1' 107 3.652 4.611 2.130
+ 4RG3 H1' 108 3.581 4.676 2.079
+ 4RG3 N9 109 3.625 4.467 2.114
+ 4RG3 C8 110 3.703 4.364 2.161
+ 4RG3 H8 111 3.793 4.382 2.219
+ 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 H1 117 3.286 4.182 1.879
+ 4RG3 C2 118 3.343 4.373 1.926
+ 4RG3 N2 119 3.244 4.425 1.852
+ 4RG3 H21 120 3.175 4.372 1.801
+ 4RG3 H22 121 3.227 4.525 1.862
+ 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 H3' 125 3.793 4.800 2.357
+ 4RG3 C2' 126 3.657 4.651 2.278
+ 4RG3 H2'1 127 3.725 4.582 2.328
+ 4RG3 O2' 128 3.531 4.656 2.342
+ 4RG3 HO'2 129 3.516 4.575 2.391
+ 4RG3 O3' 130 3.637 4.890 2.255
+ 4RG3 H3T 131 3.572 4.861 2.319
+ 1RC5 H5T 132 2.634 3.727 1.763
+ 1RC5 O5' 133 2.636 3.747 1.669
+ 1RC5 C5' 134 2.553 3.857 1.641
+ 1RC5 H5'1 135 2.466 3.850 1.706
+ 1RC5 H5'2 136 2.522 3.834 1.539
+ 1RC5 C4' 137 2.622 3.993 1.640
+ 1RC5 H4' 138 2.549 4.070 1.616
+ 1RC5 O4' 139 2.675 4.045 1.760
+ 1RC5 C1' 140 2.802 4.099 1.733
+ 1RC5 H1' 141 2.813 4.198 1.779
+ 1RC5 N1 142 2.920 4.024 1.779
+ 1RC5 C6 143 2.911 3.891 1.812
+ 1RC5 H6 144 2.820 3.836 1.799
+ 1RC5 C5 145 3.023 3.830 1.857
+ 1RC5 H5 146 3.014 3.727 1.889
+ 1RC5 C4 147 3.138 3.912 1.878
+ 1RC5 N4 148 3.247 3.861 1.938
+ 1RC5 H41 149 3.242 3.780 1.998
+ 1RC5 H42 150 3.325 3.917 1.969
+ 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 H3' 155 2.805 3.914 1.543
+ 1RC5 C2' 156 2.813 4.120 1.582
+ 1RC5 H2'1 157 2.914 4.128 1.543
+ 1RC5 O2' 158 2.747 4.241 1.551
+ 1RC5 HO'2 159 2.701 4.227 1.468
+ 1RC5 O3' 160 2.681 4.015 1.408
+ 2RG P 161 2.764 3.967 1.279
+ 2RG O1P 162 2.683 4.010 1.163
+ 2RG O2P 163 2.805 3.826 1.297
+ 2RG O5' 164 2.889 4.067 1.292
+ 2RG C5' 165 2.898 4.188 1.219
+ 2RG H5'1 166 2.814 4.253 1.243
+ 2RG H5'2 167 2.901 4.162 1.114
+ 2RG C4' 168 3.018 4.280 1.244
+ 2RG H4' 169 2.994 4.383 1.214
+ 2RG O4' 170 3.054 4.277 1.380
+ 2RG C1' 171 3.194 4.278 1.393
+ 2RG H1' 172 3.221 4.359 1.462
+ 2RG N9 173 3.245 4.158 1.461
+ 2RG C8 174 3.203 4.028 1.471
+ 2RG H8 175 3.112 4.001 1.420
+ 2RG N7 176 3.276 3.950 1.546
+ 2RG C5 177 3.382 4.031 1.584
+ 2RG C6 178 3.491 4.012 1.673
+ 2RG O6 179 3.523 3.911 1.734
+ 2RG N1 180 3.571 4.125 1.690
+ 2RG H1 181 3.654 4.117 1.746
+ 2RG C2 182 3.539 4.248 1.636
+ 2RG N2 183 3.637 4.339 1.648
+ 2RG H21 184 3.716 4.316 1.706
+ 2RG H22 185 3.629 4.427 1.598
+ 2RG N3 186 3.434 4.269 1.556
+ 2RG C4 187 3.363 4.156 1.532
+ 2RG C3' 188 3.146 4.245 1.168
+ 2RG H3' 189 3.147 4.136 1.165
+ 2RG C2' 190 3.261 4.291 1.256
+ 2RG H2'1 191 3.352 4.231 1.248
+ 2RG O2' 192 3.281 4.428 1.230
+ 2RG HO'2 193 3.371 4.444 1.262
+ 2RG O3' 194 3.141 4.299 1.038
+ 3RC P 195 3.237 4.241 0.922
+ 3RC O1P 196 3.197 4.314 0.800
+ 3RC O2P 197 3.233 4.093 0.938
+ 3RC O5' 198 3.388 4.283 0.956
+ 3RC C5' 199 3.441 4.411 0.930
+ 3RC H5'1 200 3.368 4.490 0.951
+ 3RC H5'2 201 3.461 4.427 0.824
+ 3RC C4' 202 3.566 4.437 1.012
+ 3RC H4' 203 3.579 4.546 1.014
+ 3RC O4' 204 3.547 4.388 1.143
+ 3RC C1' 205 3.675 4.358 1.193
+ 3RC H1' 206 3.695 4.426 1.276
+ 3RC N1 207 3.668 4.218 1.238
+ 3RC C6 208 3.582 4.125 1.188
+ 3RC H6 209 3.508 4.149 1.112
+ 3RC C5 210 3.577 4.001 1.241
+ 3RC H5 211 3.500 3.931 1.213
+ 3RC C4 212 3.657 3.972 1.356
+ 3RC N4 213 3.642 3.862 1.431
+ 3RC H41 214 3.571 3.795 1.407
+ 3RC H42 215 3.695 3.843 1.514
+ 3RC N3 216 3.749 4.061 1.398
+ 3RC C2 217 3.758 4.182 1.337
+ 3RC O2 218 3.837 4.261 1.389
+ 3RC C3' 219 3.695 4.382 0.951
+ 3RC H3' 220 3.675 4.281 0.916
+ 3RC C2' 221 3.777 4.373 1.080
+ 3RC H2'1 222 3.845 4.288 1.081
+ 3RC O2' 223 3.848 4.491 1.108
+ 3RC HO'2 224 3.837 4.544 1.029
+ 3RC 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 H5'1 231 4.045 4.540 0.941
+ 4RU3 H5'2 232 4.111 4.523 0.780
+ 4RU3 C4' 233 4.206 4.401 0.932
+ 4RU3 H4' 234 4.289 4.471 0.924
+ 4RU3 O4' 235 4.184 4.357 1.065
+ 4RU3 C1' 236 4.260 4.239 1.075
+ 4RU3 H1' 237 4.331 4.253 1.155
+ 4RU3 N1 238 4.174 4.122 1.103
+ 4RU3 C6 239 4.050 4.105 1.048
+ 4RU3 H6 240 4.024 4.172 0.967
+ 4RU3 C5 241 3.961 4.019 1.100
+ 4RU3 H5 242 3.860 4.011 1.063
+ 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 H3 246 4.156 3.880 1.323
+ 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 H3' 250 4.163 4.214 0.820
+ 4RU3 C2' 251 4.340 4.210 0.948
+ 4RU3 H2'1 252 4.343 4.103 0.931
+ 4RU3 O2' 253 4.472 4.258 0.958
+ 4RU3 HO'2 254 4.496 4.267 0.866
+ 4RU3 O3' 255 4.325 4.314 0.738
+ 4RU3 H3T 256 4.281 4.267 0.667
+ 5HO4 OW 257 4.162 1.101 1.896
+ 5HO4 HW2 258 4.221 1.026 1.891
+ 5HO4 HW3 259 4.077 1.063 1.919
+ 5HO4 MW4 260 4.162 1.101 1.896
+ 6HO4 OW 261 2.661 1.981 0.167
+ 6HO4 HW2 262 2.671 1.886 0.170
+ 6HO4 HW3 263 2.568 1.995 0.147
+ 6HO4 MW4 264 2.661 1.981 0.167
+ 7HO4 OW 265 2.827 1.758 3.373
+ 7HO4 HW2 266 2.769 1.694 3.332
+ 7HO4 HW3 267 2.913 1.714 3.375
+ 7HO4 MW4 268 2.827 1.758 3.373
+ 8HO4 OW 269 3.674 2.036 3.220
+ 8HO4 HW2 270 3.646 2.126 3.201
+ 8HO4 HW3 271 3.597 1.983 3.199
+ 8HO4 MW4 272 3.674 2.036 3.220
+ 9HO4 OW 273 2.398 0.101 0.569
+ 9HO4 HW2 274 2.426 0.171 0.510
+ 9HO4 HW3 275 2.458 0.029 0.550
+ 9HO4 MW4 276 2.398 0.101 0.569
+ 10HO4 OW 277 3.266 3.721 3.625
+ 10HO4 HW2 278 3.336 3.782 3.603
+ 10HO4 HW3 279 3.197 3.739 3.560
+ 10HO4 MW4 280 3.266 3.721 3.625
+ 11HO4 OW 281 1.089 5.019 0.333
+ 11HO4 HW2 282 1.097 4.926 0.357
+ 11HO4 HW3 283 1.179 5.048 0.319
+ 11HO4 MW4 284 1.089 5.019 0.333
+ 12HO4 OW 285 4.056 3.437 2.398
+ 12HO4 HW2 286 4.023 3.483 2.321
+ 12HO4 HW3 287 4.140 3.480 2.417
+ 12HO4 MW4 288 4.056 3.437 2.398
+ 13HO4 OW 289 3.318 3.921 0.051
+ 13HO4 HW2 290 3.411 3.941 0.061
+ 13HO4 HW3 291 3.290 3.970 -0.026
+ 13HO4 MW4 292 3.318 3.921 0.051
+ 14HO4 OW 293 5.842 1.508 3.122
+ 14HO4 HW2 294 5.779 1.498 3.193
+ 14HO4 HW3 295 5.903 1.575 3.154
+ 14HO4 MW4 296 5.842 1.508 3.122
+ 15HO4 OW 297 4.099 0.240 0.647
+ 15HO4 HW2 298 4.077 0.333 0.635
+ 15HO4 HW3 299 4.160 0.239 0.720
+ 15HO4 MW4 300 4.099 0.240 0.647
+ 16HO4 OW 301 1.683 4.252 0.604
+ 16HO4 HW2 302 1.758 4.200 0.573
+ 16HO4 HW3 303 1.607 4.197 0.585
+ 16HO4 MW4 304 1.683 4.252 0.604
+ 17HO4 OW 305 4.025 1.837 1.048
+ 17HO4 HW2 306 4.022 1.932 1.058
+ 17HO4 HW3 307 4.084 1.822 0.974
+ 17HO4 MW4 308 4.025 1.837 1.048
+ 18HO4 OW 309 1.037 4.918 0.896
+ 18HO4 HW2 310 1.051 4.827 0.869
+ 18HO4 HW3 311 0.978 4.954 0.830
+ 18HO4 MW4 312 1.037 4.918 0.896
+ 19HO4 OW 313 3.750 3.079 0.615
+ 19HO4 HW2 314 3.819 3.141 0.592
+ 19HO4 HW3 315 3.710 3.056 0.531
+ 19HO4 MW4 316 3.750 3.079 0.615
+ 20HO4 OW 317 5.473 2.352 3.056
+ 20HO4 HW2 318 5.532 2.279 3.072
+ 20HO4 HW3 319 5.483 2.370 2.962
+ 20HO4 MW4 320 5.473 2.352 3.056
+ 21HO4 OW 321 3.327 1.472 2.603
+ 21HO4 HW2 322 3.413 1.434 2.620
+ 21HO4 HW3 323 3.265 1.405 2.634
+ 21HO4 MW4 324 3.327 1.472 2.603
+ 22HO4 OW 325 5.165 0.979 1.122
+ 22HO4 HW2 326 5.090 0.957 1.066
+ 22HO4 HW3 327 5.242 0.963 1.067
+ 22HO4 MW4 328 5.165 0.979 1.122
+ 23HO4 OW 329 1.631 5.010 0.227
+ 23HO4 HW2 330 1.536 5.014 0.217
+ 23HO4 HW3 331 1.645 4.954 0.304
+ 23HO4 MW4 332 1.631 5.010 0.227
+ 24HO4 OW 333 3.388 0.355 1.076
+ 24HO4 HW2 334 3.360 0.368 1.166
+ 24HO4 HW3 335 3.432 0.270 1.077
+ 24HO4 MW4 336 3.388 0.355 1.076
+ 25HO4 OW 337 2.397 3.250 1.282
+ 25HO4 HW2 338 2.362 3.208 1.361
+ 25HO4 HW3 339 2.329 3.238 1.216
+ 25HO4 MW4 340 2.397 3.250 1.282
+ 26HO4 OW 341 6.770 4.605 3.023
+ 26HO4 HW2 342 6.846 4.662 3.030
+ 26HO4 HW3 343 6.768 4.557 3.106
+ 26HO4 MW4 344 6.770 4.605 3.023
+ 27HO4 OW 345 5.661 2.565 2.929
+ 27HO4 HW2 346 5.589 2.613 2.970
+ 27HO4 HW3 347 5.663 2.599 2.839
+ 27HO4 MW4 348 5.661 2.565 2.929
+ 28HO4 OW 349 1.302 4.655 0.077
+ 28HO4 HW2 350 1.380 4.689 0.122
+ 28HO4 HW3 351 1.271 4.584 0.134
+ 28HO4 MW4 352 1.302 4.655 0.077
+ 29HO4 OW 353 5.202 1.509 1.105
+ 29HO4 HW2 354 5.222 1.421 1.137
+ 29HO4 HW3 355 5.159 1.552 1.179
+ 29HO4 MW4 356 5.202 1.509 1.105
+ 30HO4 OW 357 4.606 4.891 1.067
+ 30HO4 HW2 358 4.543 4.963 1.060
+ 30HO4 HW3 359 4.667 4.906 0.995
+ 30HO4 MW4 360 4.606 4.891 1.067
+ 31HO4 OW 361 4.232 3.142 2.842
+ 31HO4 HW2 362 4.166 3.206 2.815
+ 31HO4 HW3 363 4.316 3.183 2.820
+ 31HO4 MW4 364 4.232 3.142 2.842
+ 32HO4 OW 365 6.453 1.493 3.470
+ 32HO4 HW2 366 6.397 1.562 3.506
+ 32HO4 HW3 367 6.393 1.420 3.455
+ 32HO4 MW4 368 6.453 1.493 3.470
+ 33HO4 OW 369 2.243 1.580 1.692
+ 33HO4 HW2 370 2.230 1.668 1.730
+ 33HO4 HW3 371 2.165 1.532 1.716
+ 33HO4 MW4 372 2.243 1.580 1.692
+ 3097Na NA12625 4.161 2.915 2.814
+ 3098Na NA12626 5.871 1.736 2.620
+ 3099Na NA12627 6.217 2.138 2.137
+ 3100Na NA12628 2.842 1.094 2.561
+ 3101Na NA12629 3.488 4.969 0.147
+ 3102Na NA12630 2.922 3.381 1.088
+ 3103Na NA12631 2.666 1.091 3.617
+ 3104Na NA12632 2.799 0.031 2.321
+ 3105Na NA12633 5.153 0.373 1.826
+ 3106Na NA12634 6.016 3.193 2.648
+ 3107Na NA12635 2.061 5.096 1.718
+ 3108Na NA12636 5.509 2.569 1.721
+ 3109Cl CL12637 4.322 4.124 0.361
+ 3110Cl CL12638 6.417 1.888 3.321
+ 3111Cl CL12639 2.664 0.227 1.271
+ 3112Cl CL12640 1.066 4.151 0.684
+ 3113Cl CL12641 2.126 2.069 1.628
+ 3114Cl CL12642 4.254 0.718 2.556
+ 5.16380 5.16380 3.65135 0.00000 0.00000 0.00000 0.00000 2.58190 2.58190
diff --git a/regtest/basic/rt-molinfo/test.pdb b/regtest/basic/rt-molinfo/test.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..3aad7601719ad953a605dce8443faf181ba5149f
--- /dev/null
+++ b/regtest/basic/rt-molinfo/test.pdb
@@ -0,0 +1,397 @@
+REMARK GENERATED BY TRJCONV
+TITLE Protein in water t= 0.00000
+REMARK THIS IS A SIMULATION BOX
+CRYST1 51.638 51.638 51.638 60.00 60.00 90.00 P 1 1
+MODEL 1
+ATOM 1 H5T RA5 A 1 42.440 30.900 19.180 1.00 0.00 H
+ATOM 2 O5' RA5 A 1 42.840 31.770 19.300 1.00 0.00 O
+ATOM 3 C5' RA5 A 1 44.230 31.550 19.440 1.00 0.00 C
+ATOM 4 1H5' RA5 A 1 44.470 30.580 19.010 1.00 0.00 H
+ATOM 5 2H5' RA5 A 1 44.420 31.610 20.510 1.00 0.00 H
+ATOM 6 C4' RA5 A 1 45.070 32.660 18.820 1.00 0.00 C
+ATOM 7 H4' RA5 A 1 46.070 32.520 19.230 1.00 0.00 H
+ATOM 8 O4' RA5 A 1 45.090 32.570 17.420 1.00 0.00 O
+ATOM 9 C1' RA5 A 1 44.930 33.850 16.850 1.00 0.00 C
+ATOM 10 H1' RA5 A 1 45.810 33.950 16.220 1.00 0.00 H
+ATOM 11 N9 RA5 A 1 43.550 34.140 16.440 1.00 0.00 N
+ATOM 12 C8 RA5 A 1 42.480 33.290 16.480 1.00 0.00 C
+ATOM 13 H8 RA5 A 1 42.670 32.300 16.870 1.00 0.00 H
+ATOM 14 N7 RA5 A 1 41.390 33.810 15.990 1.00 0.00 N
+ATOM 15 C5 RA5 A 1 41.800 35.040 15.480 1.00 0.00 C
+ATOM 16 C6 RA5 A 1 41.220 36.130 14.800 1.00 0.00 C
+ATOM 17 N6 RA5 A 1 39.920 36.190 14.490 1.00 0.00 N
+ATOM 18 H61 RA5 A 1 39.240 35.510 14.790 1.00 0.00 H
+ATOM 19 H62 RA5 A 1 39.560 37.100 14.240 1.00 0.00 H
+ATOM 20 N1 RA5 A 1 41.910 37.180 14.350 1.00 0.00 N
+ATOM 21 C2 RA5 A 1 43.200 37.200 14.640 1.00 0.00 C
+ATOM 22 H2 RA5 A 1 43.880 37.950 14.260 1.00 0.00 H
+ATOM 23 N3 RA5 A 1 43.860 36.320 15.370 1.00 0.00 N
+ATOM 24 C4 RA5 A 1 43.140 35.220 15.690 1.00 0.00 C
+ATOM 25 C3' RA5 A 1 44.690 34.080 19.230 1.00 0.00 C
+ATOM 26 H3' RA5 A 1 43.610 34.270 19.260 1.00 0.00 H
+ATOM 27 C2' RA5 A 1 45.300 34.770 18.010 1.00 0.00 C
+ATOM 28 1H2' RA5 A 1 44.900 35.780 17.890 1.00 0.00 H
+ATOM 29 O2' RA5 A 1 46.700 34.720 18.150 1.00 0.00 O
+ATOM 30 2HO' RA5 A 1 46.920 34.700 19.080 1.00 0.00 H
+ATOM 31 O3' RA5 A 1 45.350 34.440 20.420 1.00 0.00 O
+ATOM 32 P RG A 2 44.750 35.390 21.570 1.00 0.00 P
+ATOM 33 O1P RG A 2 45.810 35.410 22.600 1.00 0.00 O
+ATOM 34 O2P RG A 2 43.380 34.910 21.890 1.00 0.00 O
+ATOM 35 O5' RG A 2 44.720 36.880 20.970 1.00 0.00 O
+ATOM 36 C5' RG A 2 45.890 37.590 20.630 1.00 0.00 C
+ATOM 37 1H5' RG A 2 46.570 36.850 20.210 1.00 0.00 H
+ATOM 38 2H5' RG A 2 46.390 37.970 21.530 1.00 0.00 H
+ATOM 39 C4' RG A 2 45.660 38.760 19.680 1.00 0.00 C
+ATOM 40 H4' RG A 2 46.560 39.370 19.710 1.00 0.00 H
+ATOM 41 O4' RG A 2 45.190 38.390 18.400 1.00 0.00 O
+ATOM 42 C1' RG A 2 44.220 39.350 18.040 1.00 0.00 C
+ATOM 43 H1' RG A 2 44.410 39.670 17.020 1.00 0.00 H
+ATOM 44 N9 RG A 2 42.850 38.820 17.940 1.00 0.00 N
+ATOM 45 C8 RG A 2 42.260 37.760 18.570 1.00 0.00 C
+ATOM 46 H8 RG A 2 42.800 37.050 19.180 1.00 0.00 H
+ATOM 47 N7 RG A 2 41.070 37.460 18.140 1.00 0.00 N
+ATOM 48 C5 RG A 2 40.840 38.430 17.170 1.00 0.00 C
+ATOM 49 C6 RG A 2 39.680 38.760 16.430 1.00 0.00 C
+ATOM 50 O6 RG A 2 38.560 38.260 16.380 1.00 0.00 O
+ATOM 51 N1 RG A 2 39.810 39.860 15.590 1.00 0.00 N
+ATOM 52 H1 RG A 2 38.980 40.140 15.080 1.00 0.00 H
+ATOM 53 C2 RG A 2 40.950 40.630 15.560 1.00 0.00 C
+ATOM 54 N2 RG A 2 40.890 41.750 14.820 1.00 0.00 N
+ATOM 55 H21 RG A 2 39.990 41.970 14.400 1.00 0.00 H
+ATOM 56 H22 RG A 2 41.630 42.420 14.760 1.00 0.00 H
+ATOM 57 N3 RG A 2 42.050 40.390 16.280 1.00 0.00 N
+ATOM 58 C4 RG A 2 41.920 39.270 17.040 1.00 0.00 C
+ATOM 59 C3' RG A 2 44.650 39.780 20.200 1.00 0.00 C
+ATOM 60 H3' RG A 2 43.770 39.320 20.650 1.00 0.00 H
+ATOM 61 C2' RG A 2 44.230 40.570 18.960 1.00 0.00 C
+ATOM 62 1H2' RG A 2 43.240 41.010 19.090 1.00 0.00 H
+ATOM 63 O2' RG A 2 45.240 41.350 18.350 1.00 0.00 O
+ATOM 64 2HO' RG A 2 45.640 41.890 19.030 1.00 0.00 H
+ATOM 65 O3' RG A 2 45.330 40.660 21.070 1.00 0.00 O
+ATOM 66 P RC A 3 44.560 41.240 22.350 1.00 0.00 P
+ATOM 67 O1P RC A 3 45.590 41.940 23.150 1.00 0.00 O
+ATOM 68 O2P RC A 3 43.640 40.300 23.040 1.00 0.00 O
+ATOM 69 O5' RC A 3 43.620 42.360 21.680 1.00 0.00 O
+ATOM 70 C5' RC A 3 44.150 43.470 21.000 1.00 0.00 C
+ATOM 71 1H5' RC A 3 45.070 43.210 20.470 1.00 0.00 H
+ATOM 72 2H5' RC A 3 44.440 44.250 21.700 1.00 0.00 H
+ATOM 73 C4' RC A 3 43.050 44.050 20.100 1.00 0.00 C
+ATOM 74 H4' RC A 3 43.530 44.970 19.760 1.00 0.00 H
+ATOM 75 O4' RC A 3 42.480 43.120 19.210 1.00 0.00 O
+ATOM 76 C1' RC A 3 41.150 43.480 18.940 1.00 0.00 C
+ATOM 77 H1' RC A 3 41.080 43.720 17.880 1.00 0.00 H
+ATOM 78 N1 RC A 3 40.200 42.390 19.250 1.00 0.00 N
+ATOM 79 C6 RC A 3 40.480 41.300 20.030 1.00 0.00 C
+ATOM 80 H6 RC A 3 41.380 41.230 20.630 1.00 0.00 H
+ATOM 81 C5 RC A 3 39.620 40.270 19.990 1.00 0.00 C
+ATOM 82 H5 RC A 3 39.830 39.350 20.520 1.00 0.00 H
+ATOM 83 C4 RC A 3 38.430 40.330 19.190 1.00 0.00 C
+ATOM 84 N4 RC A 3 37.590 39.290 19.210 1.00 0.00 N
+ATOM 85 H41 RC A 3 37.920 38.370 19.480 1.00 0.00 H
+ATOM 86 H42 RC A 3 36.710 39.400 18.730 1.00 0.00 H
+ATOM 87 N3 RC A 3 38.160 41.400 18.430 1.00 0.00 N
+ATOM 88 C2 RC A 3 39.030 42.440 18.510 1.00 0.00 C
+ATOM 89 O2 RC A 3 38.770 43.430 17.830 1.00 0.00 O
+ATOM 90 C3' RC A 3 41.870 44.550 20.930 1.00 0.00 C
+ATOM 91 H3' RC A 3 41.560 43.890 21.740 1.00 0.00 H
+ATOM 92 C2' RC A 3 40.850 44.700 19.800 1.00 0.00 C
+ATOM 93 1H2' RC A 3 39.840 44.520 20.170 1.00 0.00 H
+ATOM 94 O2' RC A 3 40.980 45.850 18.990 1.00 0.00 O
+ATOM 95 2HO' RC A 3 41.670 46.460 19.250 1.00 0.00 H
+ATOM 96 O3' RC A 3 42.150 45.830 21.440 1.00 0.00 O
+ATOM 97 P RG3 A 4 41.550 46.340 22.850 1.00 0.00 P
+ATOM 98 O1P RG3 A 4 42.230 47.630 23.060 1.00 0.00 O
+ATOM 99 O2P RG3 A 4 41.730 45.220 23.810 1.00 0.00 O
+ATOM 100 O5' RG3 A 4 39.960 46.560 22.690 1.00 0.00 O
+ATOM 101 C5' RG3 A 4 39.610 47.620 21.820 1.00 0.00 C
+ATOM 102 1H5' RG3 A 4 40.110 47.570 20.860 1.00 0.00 H
+ATOM 103 2H5' RG3 A 4 39.900 48.570 22.260 1.00 0.00 H
+ATOM 104 C4' RG3 A 4 38.140 47.670 21.430 1.00 0.00 C
+ATOM 105 H4' RG3 A 4 37.950 48.530 20.800 1.00 0.00 H
+ATOM 106 O4' RG3 A 4 37.790 46.460 20.790 1.00 0.00 O
+ATOM 107 C1' RG3 A 4 36.520 46.110 21.300 1.00 0.00 C
+ATOM 108 H1' RG3 A 4 35.810 46.760 20.790 1.00 0.00 H
+ATOM 109 N9 RG3 A 4 36.250 44.670 21.140 1.00 0.00 N
+ATOM 110 C8 RG3 A 4 37.030 43.640 21.610 1.00 0.00 C
+ATOM 111 H8 RG3 A 4 37.930 43.820 22.190 1.00 0.00 H
+ATOM 112 N7 RG3 A 4 36.630 42.440 21.310 1.00 0.00 N
+ATOM 113 C5 RG3 A 4 35.520 42.650 20.500 1.00 0.00 C
+ATOM 114 C6 RG3 A 4 34.570 41.720 19.990 1.00 0.00 C
+ATOM 115 O6 RG3 A 4 34.570 40.500 20.000 1.00 0.00 O
+ATOM 116 N1 RG3 A 4 33.570 42.360 19.270 1.00 0.00 N
+ATOM 117 H1 RG3 A 4 32.860 41.820 18.790 1.00 0.00 H
+ATOM 118 C2 RG3 A 4 33.430 43.730 19.260 1.00 0.00 C
+ATOM 119 N2 RG3 A 4 32.440 44.250 18.520 1.00 0.00 N
+ATOM 120 H21 RG3 A 4 31.750 43.720 18.010 1.00 0.00 H
+ATOM 121 H22 RG3 A 4 32.270 45.250 18.620 1.00 0.00 H
+ATOM 122 N3 RG3 A 4 34.180 44.600 19.940 1.00 0.00 N
+ATOM 123 C4 RG3 A 4 35.240 43.990 20.500 1.00 0.00 C
+ATOM 124 C3' RG3 A 4 37.300 47.840 22.700 1.00 0.00 C
+ATOM 125 H3' RG3 A 4 37.930 48.000 23.570 1.00 0.00 H
+ATOM 126 C2' RG3 A 4 36.570 46.510 22.780 1.00 0.00 C
+ATOM 127 1H2' RG3 A 4 37.250 45.820 23.280 1.00 0.00 H
+ATOM 128 O2' RG3 A 4 35.310 46.560 23.420 1.00 0.00 O
+ATOM 129 2HO' RG3 A 4 35.160 45.750 23.910 1.00 0.00 H
+ATOM 130 O3' RG3 A 4 36.370 48.900 22.550 1.00 0.00 O
+ATOM 131 H3T RG3 A 4 35.720 48.610 23.190 1.00 0.00 H
+ATOM 132 H5T RC5 B 1 26.340 37.270 17.630 1.00 0.00 H
+ATOM 133 O5' RC5 B 1 26.360 37.470 16.690 1.00 0.00 O
+ATOM 134 C5' RC5 B 1 25.530 38.570 16.410 1.00 0.00 C
+ATOM 135 1H5' RC5 B 1 24.660 38.500 17.060 1.00 0.00 H
+ATOM 136 2H5' RC5 B 1 25.220 38.340 15.390 1.00 0.00 H
+ATOM 137 C4' RC5 B 1 26.220 39.930 16.400 1.00 0.00 C
+ATOM 138 H4' RC5 B 1 25.490 40.700 16.160 1.00 0.00 H
+ATOM 139 O4' RC5 B 1 26.750 40.450 17.600 1.00 0.00 O
+ATOM 140 C1' RC5 B 1 28.020 40.990 17.330 1.00 0.00 C
+ATOM 141 H1' RC5 B 1 28.130 41.980 17.790 1.00 0.00 H
+ATOM 142 N1 RC5 B 1 29.200 40.240 17.790 1.00 0.00 N
+ATOM 143 C6 RC5 B 1 29.110 38.910 18.120 1.00 0.00 C
+ATOM 144 H6 RC5 B 1 28.200 38.360 17.990 1.00 0.00 H
+ATOM 145 C5 RC5 B 1 30.230 38.300 18.570 1.00 0.00 C
+ATOM 146 H5 RC5 B 1 30.140 37.270 18.890 1.00 0.00 H
+ATOM 147 C4 RC5 B 1 31.380 39.120 18.780 1.00 0.00 C
+ATOM 148 N4 RC5 B 1 32.470 38.610 19.380 1.00 0.00 N
+ATOM 149 H41 RC5 B 1 32.420 37.800 19.980 1.00 0.00 H
+ATOM 150 H42 RC5 B 1 33.250 39.170 19.690 1.00 0.00 H
+ATOM 151 N3 RC5 B 1 31.470 40.410 18.440 1.00 0.00 N
+ATOM 152 C2 RC5 B 1 30.340 41.000 17.950 1.00 0.00 C
+ATOM 153 O2 RC5 B 1 30.510 42.190 17.700 1.00 0.00 O
+ATOM 154 C3' RC5 B 1 27.350 39.970 15.370 1.00 0.00 C
+ATOM 155 H3' RC5 B 1 28.050 39.140 15.430 1.00 0.00 H
+ATOM 156 C2' RC5 B 1 28.130 41.200 15.820 1.00 0.00 C
+ATOM 157 1H2' RC5 B 1 29.140 41.280 15.430 1.00 0.00 H
+ATOM 158 O2' RC5 B 1 27.470 42.410 15.510 1.00 0.00 O
+ATOM 159 2HO' RC5 B 1 27.010 42.270 14.680 1.00 0.00 H
+ATOM 160 O3' RC5 B 1 26.810 40.150 14.080 1.00 0.00 O
+ATOM 161 P RG B 2 27.640 39.670 12.790 1.00 0.00 P
+ATOM 162 O1P RG B 2 26.830 40.100 11.630 1.00 0.00 O
+ATOM 163 O2P RG B 2 28.050 38.260 12.970 1.00 0.00 O
+ATOM 164 O5' RG B 2 28.890 40.670 12.920 1.00 0.00 O
+ATOM 165 C5' RG B 2 28.980 41.880 12.190 1.00 0.00 C
+ATOM 166 1H5' RG B 2 28.140 42.530 12.430 1.00 0.00 H
+ATOM 167 2H5' RG B 2 29.010 41.620 11.140 1.00 0.00 H
+ATOM 168 C4' RG B 2 30.180 42.800 12.440 1.00 0.00 C
+ATOM 169 H4' RG B 2 29.940 43.830 12.140 1.00 0.00 H
+ATOM 170 O4' RG B 2 30.540 42.770 13.800 1.00 0.00 O
+ATOM 171 C1' RG B 2 31.940 42.780 13.930 1.00 0.00 C
+ATOM 172 H1' RG B 2 32.210 43.590 14.620 1.00 0.00 H
+ATOM 173 N9 RG B 2 32.450 41.580 14.610 1.00 0.00 N
+ATOM 174 C8 RG B 2 32.030 40.280 14.710 1.00 0.00 C
+ATOM 175 H8 RG B 2 31.120 40.010 14.200 1.00 0.00 H
+ATOM 176 N7 RG B 2 32.760 39.500 15.460 1.00 0.00 N
+ATOM 177 C5 RG B 2 33.820 40.310 15.840 1.00 0.00 C
+ATOM 178 C6 RG B 2 34.910 40.120 16.730 1.00 0.00 C
+ATOM 179 O6 RG B 2 35.230 39.110 17.340 1.00 0.00 O
+ATOM 180 N1 RG B 2 35.710 41.250 16.900 1.00 0.00 N
+ATOM 181 H1 RG B 2 36.540 41.170 17.460 1.00 0.00 H
+ATOM 182 C2 RG B 2 35.390 42.480 16.360 1.00 0.00 C
+ATOM 183 N2 RG B 2 36.370 43.390 16.480 1.00 0.00 N
+ATOM 184 H21 RG B 2 37.160 43.160 17.060 1.00 0.00 H
+ATOM 185 H22 RG B 2 36.290 44.270 15.980 1.00 0.00 H
+ATOM 186 N3 RG B 2 34.340 42.690 15.560 1.00 0.00 N
+ATOM 187 C4 RG B 2 33.630 41.560 15.320 1.00 0.00 C
+ATOM 188 C3' RG B 2 31.460 42.450 11.680 1.00 0.00 C
+ATOM 189 H3' RG B 2 31.470 41.360 11.650 1.00 0.00 H
+ATOM 190 C2' RG B 2 32.610 42.910 12.560 1.00 0.00 C
+ATOM 191 1H2' RG B 2 33.520 42.310 12.480 1.00 0.00 H
+ATOM 192 O2' RG B 2 32.810 44.280 12.300 1.00 0.00 O
+ATOM 193 2HO' RG B 2 33.710 44.440 12.620 1.00 0.00 H
+ATOM 194 O3' RG B 2 31.410 42.990 10.380 1.00 0.00 O
+ATOM 195 P RC B 3 32.370 42.410 9.220 1.00 0.00 P
+ATOM 196 O1P RC B 3 31.970 43.140 8.000 1.00 0.00 O
+ATOM 197 O2P RC B 3 32.330 40.930 9.380 1.00 0.00 O
+ATOM 198 O5' RC B 3 33.880 42.830 9.560 1.00 0.00 O
+ATOM 199 C5' RC B 3 34.410 44.110 9.300 1.00 0.00 C
+ATOM 200 1H5' RC B 3 33.680 44.900 9.510 1.00 0.00 H
+ATOM 201 2H5' RC B 3 34.610 44.270 8.240 1.00 0.00 H
+ATOM 202 C4' RC B 3 35.660 44.370 10.120 1.00 0.00 C
+ATOM 203 H4' RC B 3 35.790 45.460 10.140 1.00 0.00 H
+ATOM 204 O4' RC B 3 35.470 43.880 11.430 1.00 0.00 O
+ATOM 205 C1' RC B 3 36.750 43.580 11.930 1.00 0.00 C
+ATOM 206 H1' RC B 3 36.950 44.260 12.760 1.00 0.00 H
+ATOM 207 N1 RC B 3 36.680 42.180 12.380 1.00 0.00 N
+ATOM 208 C6 RC B 3 35.820 41.250 11.880 1.00 0.00 C
+ATOM 209 H6 RC B 3 35.080 41.490 11.120 1.00 0.00 H
+ATOM 210 C5 RC B 3 35.770 40.010 12.410 1.00 0.00 C
+ATOM 211 H5 RC B 3 35.000 39.310 12.130 1.00 0.00 H
+ATOM 212 C4 RC B 3 36.570 39.720 13.560 1.00 0.00 C
+ATOM 213 N4 RC B 3 36.420 38.620 14.310 1.00 0.00 N
+ATOM 214 H41 RC B 3 35.710 37.950 14.070 1.00 0.00 H
+ATOM 215 H42 RC B 3 36.950 38.430 15.140 1.00 0.00 H
+ATOM 216 N3 RC B 3 37.490 40.610 13.980 1.00 0.00 N
+ATOM 217 C2 RC B 3 37.580 41.820 13.370 1.00 0.00 C
+ATOM 218 O2 RC B 3 38.370 42.610 13.890 1.00 0.00 O
+ATOM 219 C3' RC B 3 36.950 43.820 9.510 1.00 0.00 C
+ATOM 220 H3' RC B 3 36.750 42.810 9.160 1.00 0.00 H
+ATOM 221 C2' RC B 3 37.770 43.730 10.800 1.00 0.00 C
+ATOM 222 1H2' RC B 3 38.450 42.880 10.810 1.00 0.00 H
+ATOM 223 O2' RC B 3 38.480 44.910 11.080 1.00 0.00 O
+ATOM 224 2HO' RC B 3 38.370 45.440 10.290 1.00 0.00 H
+ATOM 225 O3' RC B 3 37.530 44.700 8.580 1.00 0.00 O
+ATOM 226 P RU3 B 4 38.570 44.210 7.440 1.00 0.00 P
+ATOM 227 O1P RU3 B 4 38.860 45.410 6.630 1.00 0.00 O
+ATOM 228 O2P RU3 B 4 38.070 43.010 6.740 1.00 0.00 O
+ATOM 229 O5' RU3 B 4 39.850 43.750 8.300 1.00 0.00 O
+ATOM 230 C5' RU3 B 4 40.840 44.670 8.700 1.00 0.00 C
+ATOM 231 1H5' RU3 B 4 40.450 45.400 9.410 1.00 0.00 H
+ATOM 232 2H5' RU3 B 4 41.110 45.230 7.800 1.00 0.00 H
+ATOM 233 C4' RU3 B 4 42.060 44.010 9.320 1.00 0.00 C
+ATOM 234 H4' RU3 B 4 42.890 44.710 9.240 1.00 0.00 H
+ATOM 235 O4' RU3 B 4 41.840 43.570 10.650 1.00 0.00 O
+ATOM 236 C1' RU3 B 4 42.600 42.390 10.750 1.00 0.00 C
+ATOM 237 H1' RU3 B 4 43.310 42.530 11.550 1.00 0.00 H
+ATOM 238 N1 RU3 B 4 41.740 41.220 11.030 1.00 0.00 N
+ATOM 239 C6 RU3 B 4 40.500 41.050 10.480 1.00 0.00 C
+ATOM 240 H6 RU3 B 4 40.240 41.720 9.670 1.00 0.00 H
+ATOM 241 C5 RU3 B 4 39.610 40.190 11.000 1.00 0.00 C
+ATOM 242 H5 RU3 B 4 38.600 40.110 10.630 1.00 0.00 H
+ATOM 243 C4 RU3 B 4 39.970 39.240 12.020 1.00 0.00 C
+ATOM 244 O4 RU3 B 4 39.240 38.380 12.510 1.00 0.00 O
+ATOM 245 N3 RU3 B 4 41.270 39.420 12.490 1.00 0.00 N
+ATOM 246 H3 RU3 B 4 41.560 38.800 13.230 1.00 0.00 H
+ATOM 247 C2 RU3 B 4 42.140 40.420 12.080 1.00 0.00 C
+ATOM 248 O2 RU3 B 4 43.280 40.430 12.540 1.00 0.00 O
+ATOM 249 C3' RU3 B 4 42.460 42.790 8.490 1.00 0.00 C
+ATOM 250 H3' RU3 B 4 41.630 42.140 8.200 1.00 0.00 H
+ATOM 251 C2' RU3 B 4 43.400 42.100 9.480 1.00 0.00 C
+ATOM 252 1H2' RU3 B 4 43.430 41.030 9.310 1.00 0.00 H
+ATOM 253 O2' RU3 B 4 44.720 42.580 9.580 1.00 0.00 O
+ATOM 254 2HO' RU3 B 4 44.960 42.670 8.660 1.00 0.00 H
+ATOM 255 O3' RU3 B 4 43.250 43.140 7.380 1.00 0.00 O
+ATOM 256 H3T RU3 B 4 42.810 42.670 6.670 1.00 0.00 H
+ATOM 257 OW SOL C 5 41.620 11.010 18.960 1.00 0.00 O
+ATOM 258 HW2 SOL C 5 42.210 10.260 18.910 1.00 0.00 H
+ATOM 259 HW3 SOL C 5 40.770 10.630 19.190 1.00 0.00 H
+ATOM 260 MW4 SOL C 5 41.620 11.010 18.960 1.00 0.00
+ATOM 261 OW SOL C 6 26.610 19.810 1.670 1.00 0.00 O
+ATOM 262 HW2 SOL C 6 26.710 18.860 1.700 1.00 0.00 H
+ATOM 263 HW3 SOL C 6 25.680 19.950 1.470 1.00 0.00 H
+ATOM 264 MW4 SOL C 6 26.610 19.810 1.670 1.00 0.00
+ATOM 265 OW SOL C 7 28.270 17.580 33.730 1.00 0.00 O
+ATOM 266 HW2 SOL C 7 27.690 16.940 33.320 1.00 0.00 H
+ATOM 267 HW3 SOL C 7 29.130 17.140 33.750 1.00 0.00 H
+ATOM 268 MW4 SOL C 7 28.270 17.580 33.730 1.00 0.00
+ATOM 269 OW SOL C 8 36.740 20.360 32.200 1.00 0.00 O
+ATOM 270 HW2 SOL C 8 36.460 21.260 32.010 1.00 0.00 H
+ATOM 271 HW3 SOL C 8 35.970 19.830 31.990 1.00 0.00 H
+ATOM 272 MW4 SOL C 8 36.740 20.360 32.200 1.00 0.00
+ATOM 273 OW SOL C 9 23.980 1.010 5.690 1.00 0.00 O
+ATOM 274 HW2 SOL C 9 24.260 1.710 5.100 1.00 0.00 H
+ATOM 275 HW3 SOL C 9 24.580 0.290 5.500 1.00 0.00 H
+ATOM 276 MW4 SOL C 9 23.980 1.010 5.690 1.00 0.00
+ATOM 277 OW SOL C 10 32.660 37.210 36.250 1.00 0.00 O
+ATOM 278 HW2 SOL C 10 33.360 37.820 36.030 1.00 0.00 H
+ATOM 279 HW3 SOL C 10 31.970 37.390 35.600 1.00 0.00 H
+ATOM 280 MW4 SOL C 10 32.660 37.210 36.250 1.00 0.00
+ATOM 281 OW SOL C 11 10.890 50.190 3.330 1.00 0.00 O
+ATOM 282 HW2 SOL C 11 10.970 49.260 3.570 1.00 0.00 H
+ATOM 283 HW3 SOL C 11 11.790 50.480 3.190 1.00 0.00 H
+ATOM 284 MW4 SOL C 11 10.890 50.190 3.330 1.00 0.00
+ATOM 285 OW SOL C 12 40.560 34.370 23.980 1.00 0.00 O
+ATOM 286 HW2 SOL C 12 40.230 34.830 23.210 1.00 0.00 H
+ATOM 287 HW3 SOL C 12 41.400 34.800 24.170 1.00 0.00 H
+ATOM 288 MW4 SOL C 12 40.560 34.370 23.980 1.00 0.00
+ATOM 289 OW SOL C 13 33.180 39.210 0.510 1.00 0.00 O
+ATOM 290 HW2 SOL C 13 34.110 39.410 0.610 1.00 0.00 H
+ATOM 291 HW3 SOL C 13 32.900 39.700 -0.260 1.00 0.00 H
+ATOM 292 MW4 SOL C 13 33.180 39.210 0.510 1.00 0.00
+ATOM 293 OW SOL C 14 58.420 15.080 31.220 1.00 0.00 O
+ATOM 294 HW2 SOL C 14 57.790 14.980 31.930 1.00 0.00 H
+ATOM 295 HW3 SOL C 14 59.030 15.750 31.540 1.00 0.00 H
+ATOM 296 MW4 SOL C 14 58.420 15.080 31.220 1.00 0.00
+ATOM 297 OW SOL C 15 40.990 2.400 6.470 1.00 0.00 O
+ATOM 298 HW2 SOL C 15 40.770 3.330 6.350 1.00 0.00 H
+ATOM 299 HW3 SOL C 15 41.600 2.390 7.200 1.00 0.00 H
+ATOM 300 MW4 SOL C 15 40.990 2.400 6.470 1.00 0.00
+ATOM 301 OW SOL C 16 16.830 42.520 6.040 1.00 0.00 O
+ATOM 302 HW2 SOL C 16 17.580 42.000 5.730 1.00 0.00 H
+ATOM 303 HW3 SOL C 16 16.070 41.970 5.850 1.00 0.00 H
+ATOM 304 MW4 SOL C 16 16.830 42.520 6.040 1.00 0.00
+ATOM 305 OW SOL C 17 40.250 18.370 10.480 1.00 0.00 O
+ATOM 306 HW2 SOL C 17 40.220 19.320 10.580 1.00 0.00 H
+ATOM 307 HW3 SOL C 17 40.840 18.220 9.740 1.00 0.00 H
+ATOM 308 MW4 SOL C 17 40.250 18.370 10.480 1.00 0.00
+ATOM 309 OW SOL C 18 10.370 49.180 8.960 1.00 0.00 O
+ATOM 310 HW2 SOL C 18 10.510 48.270 8.690 1.00 0.00 H
+ATOM 311 HW3 SOL C 18 9.780 49.540 8.300 1.00 0.00 H
+ATOM 312 MW4 SOL C 18 10.370 49.180 8.960 1.00 0.00
+ATOM 313 OW SOL C 19 37.500 30.790 6.150 1.00 0.00 O
+ATOM 314 HW2 SOL C 19 38.190 31.410 5.920 1.00 0.00 H
+ATOM 315 HW3 SOL C 19 37.100 30.560 5.310 1.00 0.00 H
+ATOM 316 MW4 SOL C 19 37.500 30.790 6.150 1.00 0.00
+ATOM 317 OW SOL C 20 54.730 23.520 30.560 1.00 0.00 O
+ATOM 318 HW2 SOL C 20 55.320 22.790 30.720 1.00 0.00 H
+ATOM 319 HW3 SOL C 20 54.830 23.700 29.620 1.00 0.00 H
+ATOM 320 MW4 SOL C 20 54.730 23.520 30.560 1.00 0.00
+ATOM 321 OW SOL C 21 33.270 14.720 26.030 1.00 0.00 O
+ATOM 322 HW2 SOL C 21 34.130 14.340 26.200 1.00 0.00 H
+ATOM 323 HW3 SOL C 21 32.650 14.050 26.340 1.00 0.00 H
+ATOM 324 MW4 SOL C 21 33.270 14.720 26.030 1.00 0.00
+ATOM 325 OW SOL C 22 51.650 9.790 11.220 1.00 0.00 O
+ATOM 326 HW2 SOL C 22 50.900 9.570 10.660 1.00 0.00 H
+ATOM 327 HW3 SOL C 22 52.420 9.630 10.670 1.00 0.00 H
+ATOM 328 MW4 SOL C 22 51.650 9.790 11.220 1.00 0.00
+ATOM 329 OW SOL C 23 16.310 50.100 2.270 1.00 0.00 O
+ATOM 330 HW2 SOL C 23 15.360 50.140 2.170 1.00 0.00 H
+ATOM 331 HW3 SOL C 23 16.450 49.540 3.040 1.00 0.00 H
+ATOM 332 MW4 SOL C 23 16.310 50.100 2.270 1.00 0.00
+ATOM 333 OW SOL C 24 33.880 3.550 10.760 1.00 0.00 O
+ATOM 334 HW2 SOL C 24 33.600 3.680 11.660 1.00 0.00 H
+ATOM 335 HW3 SOL C 24 34.320 2.700 10.770 1.00 0.00 H
+ATOM 336 MW4 SOL C 24 33.880 3.550 10.760 1.00 0.00
+ATOM 337 OW SOL C 25 23.970 32.500 12.820 1.00 0.00 O
+ATOM 338 HW2 SOL C 25 23.620 32.080 13.610 1.00 0.00 H
+ATOM 339 HW3 SOL C 25 23.290 32.380 12.160 1.00 0.00 H
+ATOM 340 MW4 SOL C 25 23.970 32.500 12.820 1.00 0.00
+ATOM 341 OW SOL C 26 67.700 46.050 30.230 1.00 0.00 O
+ATOM 342 HW2 SOL C 26 68.460 46.620 30.300 1.00 0.00 H
+ATOM 343 HW3 SOL C 26 67.680 45.570 31.060 1.00 0.00 H
+ATOM 344 MW4 SOL C 26 67.700 46.050 30.230 1.00 0.00
+ATOM 345 OW SOL C 27 56.610 25.650 29.290 1.00 0.00 O
+ATOM 346 HW2 SOL C 27 55.890 26.130 29.700 1.00 0.00 H
+ATOM 347 HW3 SOL C 27 56.630 25.990 28.390 1.00 0.00 H
+ATOM 348 MW4 SOL C 27 56.610 25.650 29.290 1.00 0.00
+ATOM 349 OW SOL C 28 13.020 46.550 0.770 1.00 0.00 O
+ATOM 350 HW2 SOL C 28 13.800 46.890 1.220 1.00 0.00 H
+ATOM 351 HW3 SOL C 28 12.710 45.840 1.340 1.00 0.00 H
+ATOM 352 MW4 SOL C 28 13.020 46.550 0.770 1.00 0.00
+ATOM 353 OW SOL C 29 52.020 15.090 11.050 1.00 0.00 O
+ATOM 354 HW2 SOL C 29 52.220 14.210 11.370 1.00 0.00 H
+ATOM 355 HW3 SOL C 29 51.590 15.520 11.790 1.00 0.00 H
+ATOM 356 MW4 SOL C 29 52.020 15.090 11.050 1.00 0.00
+ATOM 357 OW SOL C 30 46.060 48.910 10.670 1.00 0.00 O
+ATOM 358 HW2 SOL C 30 45.430 49.630 10.600 1.00 0.00 H
+ATOM 359 HW3 SOL C 30 46.670 49.060 9.950 1.00 0.00 H
+ATOM 360 MW4 SOL C 30 46.060 48.910 10.670 1.00 0.00
+ATOM 361 OW SOL C 31 42.320 31.420 28.420 1.00 0.00 O
+ATOM 362 HW2 SOL C 31 41.660 32.060 28.150 1.00 0.00 H
+ATOM 363 HW3 SOL C 31 43.160 31.830 28.200 1.00 0.00 H
+ATOM 364 MW4 SOL C 31 42.320 31.420 28.420 1.00 0.00
+ATOM 365 OW SOL C 32 64.530 14.930 34.700 1.00 0.00 O
+ATOM 366 HW2 SOL C 32 63.970 15.620 35.060 1.00 0.00 H
+ATOM 367 HW3 SOL C 32 63.930 14.200 34.550 1.00 0.00 H
+ATOM 368 MW4 SOL C 32 64.530 14.930 34.700 1.00 0.00
+ATOM 369 OW SOL C 33 22.430 15.800 16.920 1.00 0.00 O
+ATOM 370 HW2 SOL C 33 22.300 16.680 17.300 1.00 0.00 H
+ATOM 371 HW3 SOL C 33 21.650 15.320 17.160 1.00 0.00 H
+ATOM 372 MW4 SOL C 33 22.430 15.800 16.920 1.00 0.00
+ATOM 373 NA NA C3097 41.610 29.150 28.140 1.00 0.00 Na
+ATOM 374 NA NA C3098 58.710 17.360 26.200 1.00 0.00 Na
+ATOM 375 NA NA C3099 62.170 21.380 21.370 1.00 0.00 Na
+ATOM 376 NA NA C3100 28.420 10.940 25.610 1.00 0.00 Na
+ATOM 377 NA NA C3101 34.880 49.690 1.470 1.00 0.00 Na
+ATOM 378 NA NA C3102 29.220 33.810 10.880 1.00 0.00 Na
+ATOM 379 NA NA C3103 26.660 10.910 36.170 1.00 0.00 Na
+ATOM 380 NA NA C3104 27.990 0.310 23.210 1.00 0.00 Na
+ATOM 381 NA NA C3105 51.530 3.730 18.260 1.00 0.00 Na
+ATOM 382 NA NA C3106 60.160 31.930 26.480 1.00 0.00 Na
+ATOM 383 NA NA C3107 20.610 50.960 17.180 1.00 0.00 Na
+ATOM 384 NA NA C3108 55.090 25.690 17.210 1.00 0.00 Na
+ATOM 385 CL CL C3109 43.220 41.240 3.610 1.00 0.00 Cl
+ATOM 386 CL CL C3110 64.170 18.880 33.210 1.00 0.00 Cl
+ATOM 387 CL CL C3111 26.640 2.270 12.710 1.00 0.00 Cl
+ATOM 388 CL CL C3112 10.660 41.510 6.840 1.00 0.00 Cl
+ATOM 389 CL CL C3113 21.260 20.690 16.280 1.00 0.00 Cl
+ATOM 390 CL CL C3114 42.540 7.180 25.560 1.00 0.00 Cl
+TER
+ENDMDL
diff --git a/regtest/basic/rt-molinfo/water.gro.reference b/regtest/basic/rt-molinfo/water.gro.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f58e7de48b84e980a4a2720b1b236f9379e7f943
--- /dev/null
+++ b/regtest/basic/rt-molinfo/water.gro.reference
@@ -0,0 +1,119 @@
+Made with PLUMED t=0.000000
+116
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+ 31SOL HW2 362 4.166 3.206 2.815
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+ 32SOL MW4 368 6.453 1.493 3.470
+ 33SOL OW 369 2.243 1.580 1.692
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+ 33SOL HW3 371 2.165 1.532 1.716
+ 33SOL MW4 372 2.243 1.580 1.692
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diff --git a/regtest/basic/rt63/plumed.dat b/regtest/basic/rt63/plumed.dat
index 5e62e70a273b4bbd70d227e278e3cd0b74f03e93..96253c3aeabc2c698e1a69a12faf64326862570f 100644
--- a/regtest/basic/rt63/plumed.dat
+++ b/regtest/basic/rt63/plumed.dat
@@ -18,3 +18,5 @@ RESTRAINT ARG=ps.a AT=0 SLOPE=1
RESTRAINT ARG=ps.b AT=0 SLOPE=2
RESTRAINT ARG=ps.c AT=0 SLOPE=3
+DUMPATOMS ATOMS=@protein FILE=protein.xyz
+
diff --git a/regtest/basic/rt63/protein.xyz.reference b/regtest/basic/rt63/protein.xyz.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f30286ff45f95816ea60e1a8b6c59738d94e46c6
--- /dev/null
+++ b/regtest/basic/rt63/protein.xyz.reference
@@ -0,0 +1,1608 @@
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diff --git a/regtest/basic/rt65/nucleic.xyz.reference b/regtest/basic/rt65/nucleic.xyz.reference
new file mode 100644
index 0000000000000000000000000000000000000000..25ade5537a1e47523cee62f5c67cbe8ad0e52dee
--- /dev/null
+++ b/regtest/basic/rt65/nucleic.xyz.reference
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diff --git a/regtest/basic/rt65/plumed.dat b/regtest/basic/rt65/plumed.dat
index 6365032dc62d4fff4c1c610882c68db40f51791b..600987c8b3f94ca7a8cb1b60fb3da8d59158df2b 100644
--- a/regtest/basic/rt65/plumed.dat
+++ b/regtest/basic/rt65/plumed.dat
@@ -3,3 +3,5 @@ MOLINFO STRUCTURE=AA.pdb MOLTYPE=rna
e1: TORSION ATOMS=@epsilon-1
t: METAD ARG=e1 SIGMA=0.15 PACE=1 TAU=200 DAMPFACTOR=100 TARGET=tgt_e1 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200 FILE=TARGET TEMP=300
+
+DUMPATOMS ATOMS=@nucleic FILE=nucleic.xyz
diff --git a/regtest/basic/rt7/all.xyz.reference b/regtest/basic/rt7/all.xyz.reference
new file mode 100644
index 0000000000000000000000000000000000000000..608fa3b15ded761700a42b88667fa260eeb45752
--- /dev/null
+++ b/regtest/basic/rt7/all.xyz.reference
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diff --git a/regtest/basic/rt7/physical.xyz.reference b/regtest/basic/rt7/physical.xyz.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2843247f917e3750051d0710fa29281d9a285d5b
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+X 1.623487 0.976123 -0.848794
+X 1.747142 1.719608 -0.031803
+X 2.723573 1.674717 0.955815
+X 2.500755 2.405598 0.123940
+X 1.656970 2.543918 0.718664
+X 1.787060 1.822951 1.738234
+X 2.508024 1.853235 -2.471422
+X 2.497141 2.601464 1.725334
+X 1.707172 2.638123 -2.475677
+X 1.608956 1.818293 -1.732905
+X 2.404669 1.777354 -0.861028
+X 2.501583 2.547549 -1.590925
+X 1.671481 2.647738 -0.895516
+X 1.558561 -1.699651 -0.078822
+X 2.614019 -1.615563 0.805744
+X 2.682000 -0.836303 0.002402
+X 1.701311 -0.926554 0.734799
+X 1.507440 -1.701330 1.663592
+X 2.683175 -1.633364 -2.547741
+X 2.308660 -1.074254 1.714044
+X 1.690730 -0.835284 -2.547747
+X 1.791043 -1.633919 -1.745052
+X 2.522680 -1.662164 -0.633352
+X 2.526903 -0.858189 -1.618237
+X 1.596901 -0.847954 -0.958911
+X -1.650430 -0.106719 -0.040446
+X -0.833051 -0.127341 0.824242
+X -0.828152 0.859144 -0.030486
+X -1.511659 0.891516 0.811295
+X -1.740506 0.096788 1.649708
+X -0.791007 -0.080601 2.421379
+X -0.952513 0.841487 1.732224
+X -1.988753 0.907632 -2.449156
+X -1.649219 0.199058 -1.534029
+X -0.790713 -0.147778 -0.756317
+X -0.755358 1.010137 -1.594104
+X -1.605580 1.052444 -0.938451
+X -1.721163 1.735213 0.020065
+X -0.836113 1.798413 0.745580
+X -0.697232 2.699602 0.112246
+X -1.708221 2.519960 0.910926
+X -1.615102 1.730411 1.795308
+X -0.807554 1.694327 -2.327612
+X -0.854811 2.446812 1.686211
+X -1.664260 2.517934 -2.469261
+X -1.738317 1.836823 -1.565652
+X -0.735543 1.770792 -0.632619
+X -0.822045 2.422630 -1.606379
+X -1.769906 2.521526 -0.654793
+X -1.687134 -1.744185 0.021996
+X -0.765040 -1.821721 0.951813
+X -0.949406 -0.980337 0.094593
+X -1.738077 -0.812735 1.001973
+X -1.543015 -1.717780 1.540440
+X -0.861122 -1.693229 2.420291
+X -0.927720 -0.834527 1.668474
+X -1.830548 -0.671471 2.394909
+X -1.753818 -1.769157 -1.663885
+X -0.722186 -1.785198 -0.835030
+X -0.884456 -1.151680 -1.677261
+X -1.619625 -0.948887 -0.888662
+108
+ 5.038800 5.038800 5.038800
+X -0.091367 0.052846 0.040752
+X 1.123944 0.056301 0.904094
+X 0.933246 0.860768 0.048223
+X -0.091755 0.875885 0.702348
+X -0.013792 0.256241 1.591332
+X 0.884778 0.212098 2.525338
+X 0.933715 0.825165 1.573585
+X -0.137239 0.798262 2.514986
+X -0.330436 -0.060024 -1.646087
+X 0.530603 -0.061048 -0.843235
+X 1.070373 0.826616 -1.694657
+X 0.139934 0.894944 -0.799486
+X 0.225197 1.695041 -0.091784
+X 0.793828 1.723116 0.854571
+X 0.940521 2.456439 -0.063983
+X 0.093911 2.509396 0.766706
+X -0.226741 1.633296 1.690701
+X 0.804766 1.446879 -2.600913
+X 0.818857 2.432240 1.813269
+X -0.023293 2.469743 -2.374797
+X 0.182680 1.682581 -1.690171
+X 0.931593 1.823769 -0.945177
+X 0.992449 2.703213 -1.732766
+X 0.053309 2.479129 -0.741922
+X 0.204859 -1.804874 -0.102071
+X 0.963914 -1.729178 0.727171
+X 0.763801 -0.867138 -0.168198
+X 0.209607 -0.713761 0.876543
+X 0.272828 -1.633640 1.551771
+X 0.897946 -1.630077 -2.540364
+X 0.887973 -0.709742 1.738690
+X 0.018398 -0.862190 -2.605005
+X 0.038546 -1.757503 -1.634498
+X 0.850892 -1.608106 -0.961724
+X 0.852524 -0.880987 -1.780311
+X -0.021862 -0.917035 -1.029285
+X 1.569538 -0.065052 -0.201168
+X 2.395395 -0.220384 0.976367
+X 2.703421 0.695080 0.080928
+X 1.972579 0.715624 0.821934
+X 1.674272 0.098250 1.787911
+X 2.419381 0.031060 -2.441625
+X 2.504499 0.959376 1.717216
+X 1.903286 0.922799 -2.314277
+X 1.821329 0.145480 -1.589486
+X 2.697088 -0.007054 -0.789185
+X 2.558627 0.940251 -1.438033
+X 1.641148 0.954936 -0.809036
+X 1.722146 1.675841 -0.024975
+X 2.712258 1.679658 0.961383
+X 2.472624 2.437292 0.149347
+X 1.641103 2.545643 0.746242
+X 1.783148 1.850324 1.725791
+X 2.507534 1.883266 -2.413925
+X 2.500490 2.616961 1.712985
+X 1.766921 2.696199 -2.480745
+X 1.625662 1.773285 -1.727677
+X 2.402767 1.849886 -0.847061
+X 2.494394 2.569258 -1.613869
+X 1.661984 2.626630 -0.892988
+X 1.614320 -1.702040 -0.091982
+X 2.549976 -1.648788 0.804364
+X 2.675494 -0.811832 0.020191
+X 1.698315 -0.959730 0.710401
+X 1.489013 -1.698686 1.624769
+X 2.656856 -1.637792 -2.455324
+X 2.265438 -1.124479 1.713062
+X 1.708048 -0.854087 -2.522527
+X 1.762414 -1.622949 -1.764444
+X 2.537404 -1.662430 -0.635264
+X 2.598827 -0.850196 -1.605351
+X 1.586794 -0.873475 -0.959890
+X -1.623991 -0.105863 0.043322
+X -0.857627 -0.104198 0.845631
+X -0.777217 0.860538 -0.007987
+X -1.519644 0.916666 0.861263
+X -1.701008 0.053707 1.651609
+X -0.786698 -0.106051 2.392634
+X -0.909238 0.858901 1.765556
+X -2.032618 0.906181 -2.424540
+X -1.647783 0.213155 -1.518146
+X -0.788343 -0.199037 -0.736388
+X -0.749265 1.024873 -1.596230
+X -1.642646 1.066064 -0.887191
+X -1.645627 1.749062 0.038298
+X -0.823851 1.802030 0.736983
+X -0.728632 2.638695 0.078705
+X -1.640029 2.494175 0.895329
+X -1.608335 1.729408 1.844806
+X -0.853048 1.734496 -2.332371
+X -0.867814 2.442629 1.682918
+X -1.657268 2.478067 -2.444949
+X -1.765477 1.905499 -1.595056
+X -0.820203 1.767849 -0.617938
+X -0.833341 2.460003 -1.549153
+X -1.754042 2.575381 -0.671785
+X -1.643736 -1.772552 0.041078
+X -0.712579 -1.823970 0.927977
+X -0.904670 -1.015550 0.060809
+X -1.745079 -0.806246 1.040294
+X -1.543026 -1.687344 1.555847
+X -0.839232 -1.660999 2.413486
+X -0.917611 -0.828290 1.680114
+X -1.739176 -0.650017 2.363404
+X -1.753449 -1.823457 -1.642584
+X -0.734393 -1.789308 -0.809391
+X -0.897959 -1.163265 -1.746028
+X -1.626502 -0.941992 -0.845934
diff --git a/regtest/basic/rt7/plumed.dat b/regtest/basic/rt7/plumed.dat
index ebee821ac9b1d3b0443edf1ffae35e62225d55b8..e97de1f9ca93877644a20ee50a448856795ada67 100644
--- a/regtest/basic/rt7/plumed.dat
+++ b/regtest/basic/rt7/plumed.dat
@@ -9,5 +9,10 @@ DUMPATOMS ATOMS=1-108,c1,c2 STRIDE=10 FILE=wrap.xyz
WRAPAROUND ATOMS=1-108 AROUND=1 GROUPBY=12
DUMPATOMS ATOMS=1-108 STRIDE=10 FILE=wrap2.xyz
+DUMPATOMS ATOMS=@allatoms STRIDE=1 FILE=all.xyz
+DUMPATOMS ATOMS=@mdatoms STRIDE=1 FILE=physical.xyz
+virtuals: GROUP ATOMS=@allatoms REMOVE=@mdatoms
+DUMPATOMS ATOMS=virtuals STRIDE=1 FILE=virtual.xyz
+
ENDPLUMED
diff --git a/regtest/basic/rt7/virtual.xyz.reference b/regtest/basic/rt7/virtual.xyz.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f0dd69ce0dfb300665e2c499e67a0725d6fd0824
--- /dev/null
+++ b/regtest/basic/rt7/virtual.xyz.reference
@@ -0,0 +1,20 @@
+2
+ 5.038800 5.038800 5.038800
+X 0.414052 0.350024 1.757001
+X 0.438406 1.917876 0.617801
+2
+ 5.038800 5.038800 5.038800
+X 0.404846 0.358287 1.753576
+X 0.449468 1.939904 0.613203
+2
+ 5.038800 5.038800 5.038800
+X 0.389438 0.360910 1.752794
+X 0.450222 1.937148 0.620901
+2
+ 5.038800 5.038800 5.038800
+X 0.379268 0.366803 1.753411
+X 0.463392 1.912382 1.891768
+2
+ 5.038800 5.038800 5.038800
+X 0.374170 0.381650 1.748894
+X 0.483705 1.882218 1.907356
diff --git a/src/core/ActionAtomistic.cpp b/src/core/ActionAtomistic.cpp
index bef9c25c143e2dea2cbb6789a9bbfbc6a071c5ab..baba14a59ff9e54a273549c83712ed6e85cb7ef6 100644
--- a/src/core/ActionAtomistic.cpp
+++ b/src/core/ActionAtomistic.cpp
@@ -174,14 +174,26 @@ void ActionAtomistic::interpretAtomList( std::vector<std::string>& strings, std:
if(ok) t.push_back(atom);
// here we check if this is a special symbol for MOLINFO
if( !ok && strings[i].compare(0,1,"@")==0 ) {
- std::size_t dot=strings[i].find_first_of("@"); std::string symbol=strings[i].substr(dot+1);
- vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
- if( moldat.size()>0 ) {
- vector<AtomNumber> atom_list; moldat[0]->interpretSymbol( symbol, atom_list );
- if( atom_list.size()>0 ) { ok=true; t.insert(t.end(),atom_list.begin(),atom_list.end()); }
- else { error(strings[i] + " is not a label plumed knows"); }
+ std::string symbol=strings[i].substr(1);
+ if(symbol=="allatoms") {
+ const auto n=plumed.getAtoms().getNatoms() + plumed.getAtoms().getNVirtualAtoms();
+ t.reserve(t.size()+n);
+ for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i));
+ ok=true;
+ } else if(symbol=="mdatoms") {
+ const auto n=plumed.getAtoms().getNatoms();
+ t.reserve(t.size()+n);
+ for(unsigned i=0; i<n; i++) t.push_back(AtomNumber::index(i));
+ ok=true;
} else {
- error("atoms specified using @ symbol but no MOLINFO was available");
+ vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
+ if( moldat.size()>0 ) {
+ vector<AtomNumber> atom_list; moldat[0]->interpretSymbol( symbol, atom_list );
+ if( atom_list.size()>0 ) { ok=true; t.insert(t.end(),atom_list.begin(),atom_list.end()); }
+ else { error(strings[i] + " is not a label plumed knows"); }
+ } else {
+ error("atoms specified using @ symbol but no MOLINFO was available");
+ }
}
}
// here we check if the atom name is the name of a group
diff --git a/src/core/Atoms.h b/src/core/Atoms.h
index 98dc1557d7da5a24f5f044f75392bc06ed96ac08..75ee16f5f6641d1e71fcbcd4a26403c5b31ef4c9 100644
--- a/src/core/Atoms.h
+++ b/src/core/Atoms.h
@@ -163,7 +163,8 @@ public:
double getKbT()const;
void setNatoms(int);
- const int & getNatoms()const;
+ const int getNatoms()const;
+ const int getNVirtualAtoms()const;
const long int& getDdStep()const;
const std::vector<int>& getGatindex()const;
@@ -234,10 +235,15 @@ public:
};
inline
-const int & Atoms::getNatoms()const {
+const int Atoms::getNatoms()const {
return natoms;
}
+inline
+const int Atoms::getNVirtualAtoms()const {
+ return virtualAtomsActions.size();
+}
+
inline
const long int& Atoms::getDdStep()const {
return ddStep;
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
index 7940a61cc14c3a17edfb5341c9c7a2834a1f1ed1..000dd46b4ce918f45eee7e357ebd7df4a0063c9b 100644
--- a/src/setup/MolInfo.cpp
+++ b/src/setup/MolInfo.cpp
@@ -50,8 +50,23 @@ for known residues from these three types of molecule. In other words, this is a
historical reasons and to allow future extensions where alternative lists will be provided.
As of now, you can just ignore this keyoword.
-Using MOLINFO with a protein's or nucleic acid's pdb extends the possibility of atoms selection using the @ special
-symbol in the form
+Using \ref MOLINFO extends the possibility of atoms selection using the @ special
+symbol. The following shortcuts are available that do not refer to one specific residue:
+
+\verbatim
+@nucleic : all atoms that are part of a DNA or RNA molecule
+@protein : all atoms that are part of a protein
+@water : all water molecules
+@ions : all the ions
+@hydrogens : all hydrogen atoms (those for which the first non-number in the name is a H)
+@nonhydrogens : all non hydrogen atoms (those for which the first non-number in the name is not a H)
+\endverbatim
+
+\warning
+Be careful since these choices are based on common names used in PDB files. Always check if
+the selected atoms are correct.
+
+In addition, atoms from a specific residue can be selected with a symbol in this form:
\verbatim
@"definition"-chain_residuenum
@@ -121,6 +136,10 @@ should not be used on 5' end residue.
Furthermore it is also possible to pick single atoms using the syntax
`atom-chain_residuenum`, `@atom-chainresiduenum` or `@atom-residuenum`.
+As of PLUMED 2.5, this also works when the residue is not a protein/rna/dna residue.
+For instance, `@OW-100` will select oxygen of water molecule with residue number 100.
+
+Finally, notice that other shortcuts are available even when not using the \ref MOLINFO command (see \ref atomSpecs).
\warning If a residue-chain is repeated twice in the reference pdb only the first entry will be selected.
@@ -154,12 +173,12 @@ PRINT ARG=hb1,hb2,hb3
This example use MOLINFO to calculate torsions angles
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
PRINT ARG=t1,t2 FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/tools/MolDataClass.cpp b/src/tools/MolDataClass.cpp
index ebe1dba42159b817559268181689838b3d5567b7..576105767f7f2a5bbe9bec468e71bee0b828b1d2 100644
--- a/src/tools/MolDataClass.cpp
+++ b/src/tools/MolDataClass.cpp
@@ -140,6 +140,22 @@ bool MolDataClass::allowedResidue( const std::string& type, const std::string& r
else if(residuename=="RC3") return true;
else if(residuename=="RCN") return true;
else return false;
+ } else if( type=="water" ) {
+ if(residuename=="SOL") return true;
+ if(residuename=="WAT") return true;
+ return false;
+ } else if( type=="ion" ) {
+ if(residuename=="IB+") return true;
+ if(residuename=="CA") return true;
+ if(residuename=="CL") return true;
+ if(residuename=="NA") return true;
+ if(residuename=="MG") return true;
+ if(residuename=="K") return true;
+ if(residuename=="RB") return true;
+ if(residuename=="CS") return true;
+ if(residuename=="LI") return true;
+ if(residuename=="ZN") return true;
+ return false;
}
return false;
}
@@ -203,7 +219,75 @@ void MolDataClass::specialSymbol( const std::string& type, const std::string& sy
// psi-4_321 is psi torsion of residue 321 of chain 4
// psi-A_321 is equivalent to psi-A321
numbers.resize(0);
+
+// special cases:
+ if(symbol=="protein") {
+ const auto & all = mypdb.getAtomNumbers();
+ for(auto a : all) {
+ auto resname=mypdb.getResidueName(a);
+ Tools::stripLeadingAndTrailingBlanks(resname);
+ if(allowedResidue("protein",resname)) numbers.push_back(a);
+ }
+ return;
+ }
+
+ if(symbol=="nucleic") {
+ const auto & all = mypdb.getAtomNumbers();
+ for(auto a : all) {
+ auto resname=mypdb.getResidueName(a);
+ Tools::stripLeadingAndTrailingBlanks(resname);
+ if(allowedResidue("dna",resname) || allowedResidue("rna",resname)) numbers.push_back(a);
+ }
+ return;
+ }
+
+ if(symbol=="ions") {
+ const auto & all = mypdb.getAtomNumbers();
+ for(auto a : all) {
+ auto resname=mypdb.getResidueName(a);
+ Tools::stripLeadingAndTrailingBlanks(resname);
+ if(allowedResidue("ion",resname)) numbers.push_back(a);
+ }
+ return;
+ }
+
+ if(symbol=="water") {
+ const auto & all = mypdb.getAtomNumbers();
+ for(auto a : all) {
+ auto resname=mypdb.getResidueName(a);
+ Tools::stripLeadingAndTrailingBlanks(resname);
+ if(allowedResidue("water",resname)) numbers.push_back(a);
+ }
+ return;
+ }
+
+ if(symbol=="hydrogens") {
+ const auto & all = mypdb.getAtomNumbers();
+ for(auto a : all) {
+ auto atomname=mypdb.getAtomName(a);
+ Tools::stripLeadingAndTrailingBlanks(atomname);
+ auto notnumber=atomname.find_first_not_of("0123456789");
+ if(notnumber!=std::string::npos && atomname[notnumber]=='H') numbers.push_back(a);
+ }
+ return;
+ }
+
+ if(symbol=="nonhydrogens") {
+ const auto & all = mypdb.getAtomNumbers();
+ for(auto a : all) {
+ auto atomname=mypdb.getAtomName(a);
+ Tools::stripLeadingAndTrailingBlanks(atomname);
+ auto notnumber=atomname.find_first_not_of("0123456789");
+ if(notnumber!=std::string::npos && atomname[notnumber]=='H') {
+ } else numbers.push_back(a);
+ }
+ return;
+ }
+
+
std::size_t dash=symbol.find_first_of('-');
+ if(dash==std::string::npos) plumed_error() << "Unrecognized symbol "<<symbol;
+
std::size_t firstunderscore=symbol.find_first_of('_',dash+1);
std::size_t firstnum=symbol.find_first_of("0123456789",dash+1);
std::string name=symbol.substr(0,dash);
@@ -404,7 +488,7 @@ void MolDataClass::specialSymbol( const std::string& type, const std::string& sy
numbers.push_back(mypdb.getNamedAtomFromResidueAndChain("C4",resnum,chainid));
} else plumed_error();
} else numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(name,resnum,chainid));
- }
+ } else numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(name,resnum,chainid));
}
else {
plumed_merror(type + " is not a valid molecule type");
diff --git a/user-doc/Group.md b/user-doc/Group.md
index 5472a030897205221a2a107fa02935d06a4c8cba..46c470cb291cf394a52a54254db2159fd7fadc6c 100644
--- a/user-doc/Group.md
+++ b/user-doc/Group.md
@@ -8,11 +8,24 @@ atoms are specified using their numerical indices in the molecular dynamics inpu
In PLUMED lists of atoms can be either provided directly inside the definition of each collective variable, or
predefined as a \subpage GROUP that can be reused multiple times. Lists of atoms can be written as:
-- comma separated lists of numbers (GROUP ATOMS=10,11,15,20 LABEL=g1)
-- numerical ranges. So GROUP ATOMS=10-20 LABEL=g2 is equivalent to GROUP ATOMS=10,11,12,13,14,15,16,17,18,19,20 LABEL=g2
-- numerical ranges with a stride. So GROUP ATOMS=10-100:10 LABEL=g3 is equivalent to GROUP ATOMS=10,20,30,40,50,60,70,80,90,100 LABEL=g3
-- atoms ranges with a negative stride. So GROUP ATOMS=100-10:-10 LABEL=g4 is equivalent to GROUP ATOMS=100,90,80,70,60,50,40,30,20,10 LABEL=g4
-- all the above methods together. For example GROUP ATOMS=1,2,10-20,40-60:5,100-70:-2 LABEL=g5.
+- comma separated lists of numbers (`GROUP ATOMS=10,11,15,20 LABEL=g1`)
+- numerical ranges. So `GROUP ATOMS=10-20 LABEL=g2` is equivalent to `GROUP ATOMS=10,11,12,13,14,15,16,17,18,19,20 LABEL=g2`
+- numerical ranges with a stride. So `GROUP ATOMS=10-100:10 LABEL=g3 is equivalent to `GROUP ATOMS=10,20,30,40,50,60,70,80,90,100 LABEL=g3`
+- atoms ranges with a negative stride. So `GROUP ATOMS=100-10:-10 LABEL=g4 is equivalent to `GROUP ATOMS=100,90,80,70,60,50,40,30,20,10 LABEL=g4`
+
+In addition, there are a few shortcuts that can be used:
+
+- `@mdatoms` indicate all the physical atoms present in the MD engine (e.g. `DUMPATOMS ATOMS=@mdatoms`).
+- `@allatoms` indicates all atoms, including \ref vatoms "those defined only in PLUMED" (e.g. `DUMPATOMS ATOMS=@allatoms`).
+
+The list of the virtual atoms defined in PLUMED can be obtained dy difference with `GROUP ATOMS=@allatoms REMOVE=@mdatoms`.
+
+Other shortcuts are available if you loaded the structure of the molecule using the \ref MOLINFO command.
+
+All the above methods can be combined just putting one name after the other separated by a comma:
+\plumedfile
+DUMPATOMS ATOMS=1,2,10-20,40-60:5,100-70:-2 LABEL=g5 FILE=test.xyz
+\endplumedfile
Some collective variable must accept a fixed number of atoms, for example a \ref DISTANCE is calculated
using two atoms only, an \ref ANGLE is calcuated using either 3 or 4 atoms and \ref TORSION is calculated using 4 atoms.