diff --git a/regtest/basic/rt65/AA.pdb b/regtest/basic/rt65/AA.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..7259a480a8559a8528c6277d155d2ed84ae9bc22
--- /dev/null
+++ b/regtest/basic/rt65/AA.pdb
@@ -0,0 +1,71 @@
+TITLE Great Red Owns Many ACres of Sand
+REMARK THIS IS A SIMULATION BOX
+CRYST1 6.958 11.030 10.714 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 H5T A 1 14.820 -3.670 5.260 1.00 0.00
+ATOM 2 O5' A 1 15.280 -2.790 5.160 1.00 0.00
+ATOM 3 C5' A 1 16.340 -2.690 6.140 1.00 0.00
+ATOM 4 1H5' A 1 17.000 -3.430 5.990 1.00 0.00
+ATOM 5 2H5' A 1 15.960 -2.760 7.060 1.00 0.00
+ATOM 6 C4' A 1 16.940 -1.350 5.900 1.00 0.00
+ATOM 7 H4' A 1 17.680 -1.280 6.580 1.00 0.00
+ATOM 8 O4' A 1 17.430 -1.280 4.600 1.00 0.00
+ATOM 9 C1' A 1 17.500 0.110 4.240 1.00 0.00
+ATOM 10 H1' A 1 18.450 0.400 4.070 1.00 0.00
+ATOM 11 N9 A 1 16.660 0.250 3.040 1.00 0.00
+ATOM 12 C8 A 1 15.860 -0.690 2.450 1.00 0.00
+ATOM 13 H8 A 1 15.740 -1.610 2.820 1.00 0.00
+ATOM 14 N7 A 1 15.260 -0.280 1.380 1.00 0.00
+ATOM 15 C5 A 1 15.710 1.020 1.230 1.00 0.00
+ATOM 16 C6 A 1 15.450 2.020 0.250 1.00 0.00
+ATOM 17 N6 A 1 14.640 1.860 -0.780 1.00 0.00
+ATOM 18 H61 A 1 14.160 0.990 -0.910 1.00 0.00
+ATOM 19 H62 A 1 14.510 2.600 -1.430 1.00 0.00
+ATOM 20 N1 A 1 16.090 3.170 0.480 1.00 0.00
+ATOM 21 C2 A 1 16.910 3.400 1.530 1.00 0.00
+ATOM 22 H2 A 1 17.340 4.300 1.590 1.00 0.00
+ATOM 23 N3 A 1 17.200 2.530 2.470 1.00 0.00
+ATOM 24 C4 A 1 16.570 1.360 2.260 1.00 0.00
+ATOM 25 C3' A 1 15.940 -0.160 5.930 1.00 0.00
+ATOM 26 H3' A 1 15.040 -0.310 5.530 1.00 0.00
+ATOM 27 C2' A 1 16.900 0.910 5.350 1.00 0.00
+ATOM 28 1H2' A 1 16.600 1.820 5.060 1.00 0.00
+ATOM 29 O2' A 1 17.840 1.060 6.410 1.00 0.00
+ATOM 30 2HO' A 1 17.420 1.600 7.150 1.00 0.00
+ATOM 31 O3' A 1 15.700 0.220 7.290 1.00 0.00
+ATOM 32 P A 2 14.280 0.530 7.900 1.00 0.00
+ATOM 33 O1P A 2 14.390 -0.010 9.290 1.00 0.00
+ATOM 34 O2P A 2 13.160 -0.100 7.150 1.00 0.00
+ATOM 35 O5' A 2 14.210 2.130 7.830 1.00 0.00
+ATOM 36 C5' A 2 15.380 2.910 7.550 1.00 0.00
+ATOM 37 1H5' A 2 15.960 2.390 6.930 1.00 0.00
+ATOM 38 2H5' A 2 15.860 3.070 8.410 1.00 0.00
+ATOM 39 C4' A 2 15.050 4.200 6.950 1.00 0.00
+ATOM 40 H4' A 2 15.630 4.770 7.540 1.00 0.00
+ATOM 41 O4' A 2 15.470 4.270 5.630 1.00 0.00
+ATOM 42 C1' A 2 14.600 5.120 4.840 1.00 0.00
+ATOM 43 H1' A 2 15.060 5.780 4.250 1.00 0.00
+ATOM 44 N9 A 2 13.880 4.270 3.880 1.00 0.00
+ATOM 45 C8 A 2 13.540 2.950 4.120 1.00 0.00
+ATOM 46 H8 A 2 13.720 2.490 4.980 1.00 0.00
+ATOM 47 N7 A 2 12.960 2.370 3.100 1.00 0.00
+ATOM 48 C5 A 2 12.920 3.360 2.120 1.00 0.00
+ATOM 49 C6 A 2 12.390 3.330 0.800 1.00 0.00
+ATOM 50 N6 A 2 11.840 2.270 0.240 1.00 0.00
+ATOM 51 H61 A 2 11.780 1.410 0.740 1.00 0.00
+ATOM 52 H62 A 2 11.490 2.330 -0.690 1.00 0.00
+ATOM 53 N1 A 2 12.470 4.520 0.120 1.00 0.00
+ATOM 54 C2 A 2 13.040 5.620 0.710 1.00 0.00
+ATOM 55 H2 A 2 13.080 6.450 0.160 1.00 0.00
+ATOM 56 N3 A 2 13.560 5.710 1.940 1.00 0.00
+ATOM 57 C4 A 2 13.470 4.520 2.580 1.00 0.00
+ATOM 58 C3' A 2 13.660 4.790 6.980 1.00 0.00
+ATOM 59 H3' A 2 12.960 4.060 6.950 1.00 0.00
+ATOM 60 C2' A 2 13.760 5.840 5.850 1.00 0.00
+ATOM 61 1H2' A 2 12.940 6.250 5.450 1.00 0.00
+ATOM 62 O2' A 2 14.540 6.880 6.470 1.00 0.00
+ATOM 63 2HO' A 2 13.980 7.360 7.150 1.00 0.00
+ATOM 64 O3' A 2 13.300 5.500 8.180 1.00 0.00
+ATOM 65 H3T A 2 12.360 5.840 8.100 1.00 0.00
+TER
+ENDMDL
diff --git a/regtest/basic/rt65/Makefile b/regtest/basic/rt65/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt65/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt65/TARGET.reference b/regtest/basic/rt65/TARGET.reference
new file mode 100644
index 0000000000000000000000000000000000000000..95aa8528f8135c610d275207b44d6300870a7fc6
--- /dev/null
+++ b/regtest/basic/rt65/TARGET.reference
@@ -0,0 +1,13 @@
+#! FIELDS time e1 sigma_e1 height biasf
+#! SET multivariate false
+#! SET min_e1 -pi
+#! SET max_e1 pi
+ 0.002 -1.903205551688819 0.15 9.109750009330055e-06 1
+ 0.004 -2.96314509497333 0.15 1.185709146847737e-05 1
+ 0.006 -2.563611512401551 0.15 3.459682279642131e-06 1
+ 0.008 -3.120966152841994 0.15 2.627063088737373e-05 1
+ 0.01 -2.640309461910613 0.15 3.857669512410835e-06 1
+ 0.012 -2.981598623047649 0.15 1.18570902777194e-05 1
+ 0.014 -1.30629526983071 0.15 2.684491613922633e-05 1
+ 0.016 -2.503951571795555 0.15 3.399120208955464e-06 1
+ 0.018 -3.014247277468189 0.15 1.387646340580046e-05 1
diff --git a/regtest/basic/rt65/config b/regtest/basic/rt65/config
new file mode 100644
index 0000000000000000000000000000000000000000..bd5f5c17c4a1d494bff6b6c49556ee0fb2c6f792
--- /dev/null
+++ b/regtest/basic/rt65/config
@@ -0,0 +1,2 @@
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 1 --timestep 0.002 --ixyz trajectory.xyz"
diff --git a/regtest/basic/rt65/plumed.dat b/regtest/basic/rt65/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..6365032dc62d4fff4c1c610882c68db40f51791b
--- /dev/null
+++ b/regtest/basic/rt65/plumed.dat
@@ -0,0 +1,5 @@
+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
diff --git a/regtest/basic/rt65/tgt_e1 b/regtest/basic/rt65/tgt_e1
new file mode 100644
index 0000000000000000000000000000000000000000..c625de5ce34191dc56db5127735f22c1e40acad2
--- /dev/null
+++ b/regtest/basic/rt65/tgt_e1
@@ -0,0 +1,205 @@
+#! FIELDS e1 t.target der_e1
+#! SET min_e1 -pi
+#! SET max_e1 pi
+#! SET nbins_e1 200
+#! SET periodic_e1 true
+ -3.14159 5.10076 -12.70892
+ -3.11018 4.70239 -12.67962
+ -3.07876 4.30407 -12.68027
+ -3.04734 3.90566 -12.65820
+ -3.01593 3.50873 -12.56070
+ -2.98451 3.11645 -12.34584
+ -2.95310 2.73302 -11.98905
+ -2.92168 2.36315 -11.48303
+ -2.89026 2.01152 -10.83462
+ -2.85885 1.68239 -10.06301
+ -2.82743 1.37924 -9.19536
+ -2.79602 1.10463 -8.25853
+ -2.76460 0.86035 -7.27827
+ -2.73319 0.64733 -6.27846
+ -2.70177 0.46586 -5.27871
+ -2.67035 0.31565 -4.29520
+ -2.63894 0.19598 -3.33913
+ -2.60752 0.10585 -2.41815
+ -2.57611 0.04405 -1.53788
+ -2.54469 0.00922 -0.70101
+ -2.51327 0.00000 0.09104
+ -2.48186 0.01494 0.83725
+ -2.45044 0.05261 1.53656
+ -2.41903 0.11149 2.18707
+ -2.38761 0.19002 2.78648
+ -2.35619 0.28657 3.33221
+ -2.32478 0.39939 3.82147
+ -2.29336 0.52667 4.25183
+ -2.26195 0.66654 4.62342
+ -2.23053 0.81717 4.93553
+ -2.19911 0.97665 5.18839
+ -2.16770 1.14317 5.38294
+ -2.13628 1.31487 5.51695
+ -2.10487 1.48981 5.58462
+ -2.07345 1.66576 5.57692
+ -2.04203 1.84022 5.48097
+ -2.01062 2.01014 5.28380
+ -1.97920 2.17221 4.97850
+ -1.94779 2.32295 4.56436
+ -1.91637 2.45899 4.05604
+ -1.88496 2.57780 3.48558
+ -1.85354 2.67800 2.90046
+ -1.82212 2.76004 2.35978
+ -1.79071 2.82627 1.92248
+ -1.75929 2.88083 1.64450
+ -1.72788 2.92960 1.56915
+ -1.69646 2.97943 1.71195
+ -1.66504 3.03716 2.07025
+ -1.63363 3.10950 2.62387
+ -1.60221 3.20203 3.33816
+ -1.57080 3.31925 4.17143
+ -1.53938 3.46413 5.07054
+ -1.50796 3.63784 5.97985
+ -1.47655 3.83984 6.84656
+ -1.44513 4.06801 7.62050
+ -1.41372 4.31866 8.25743
+ -1.38230 4.58685 8.73061
+ -1.35088 4.86722 9.03758
+ -1.31947 5.15470 9.20074
+ -1.28805 5.44532 9.27486
+ -1.25664 5.73745 9.33973
+ -1.22522 6.03215 9.47554
+ -1.19381 6.33282 9.75711
+ -1.16239 6.64521 10.22904
+ -1.13097 6.97553 10.90943
+ -1.09956 7.33067 11.77148
+ -1.06814 7.71514 12.75565
+ -1.03673 8.13212 13.79332
+ -1.00531 8.58181 14.77995
+ -0.97389 9.06078 15.61190
+ -0.94248 9.56273 16.16983
+ -0.91106 10.07676 16.32518
+ -0.87965 10.58848 16.02464
+ -0.84823 11.08362 15.28715
+ -0.81681 11.54900 14.17647
+ -0.78540 11.97436 12.86211
+ -0.75398 12.35715 11.57633
+ -0.72257 12.70172 10.55300
+ -0.69115 13.02022 9.88103
+ -0.65973 13.32257 9.50496
+ -0.62832 13.61742 9.40240
+ -0.59690 13.91333 9.43842
+ -0.56549 14.21046 9.44831
+ -0.53407 14.50698 9.34280
+ -0.50265 14.79749 9.04752
+ -0.47124 15.07546 8.52664
+ -0.43982 15.33323 7.74502
+ -0.40841 15.56209 6.80145
+ -0.37699 15.76058 5.80952
+ -0.34558 15.92712 4.90263
+ -0.31416 16.06862 4.15626
+ -0.28274 16.18826 3.55378
+ -0.25133 16.29191 2.98214
+ -0.21991 16.37564 2.29118
+ -0.18850 16.43587 1.31572
+ -0.15708 16.45830 -0.09998
+ -0.12566 16.42959 -1.82144
+ -0.09425 16.34386 -3.60730
+ -0.06283 16.20294 -5.18707
+ -0.03142 16.01795 -6.30761
+ 0.00000 15.80662 -6.83201
+ 0.03142 15.58868 -6.76985
+ 0.06283 15.38125 -6.23660
+ 0.09425 15.19682 -5.36388
+ 0.12566 15.04423 -4.28282
+ 0.15708 14.92772 -3.11155
+ 0.18850 14.84872 -1.93712
+ 0.21991 14.80601 -0.84119
+ 0.25133 14.79587 0.12393
+ 0.28274 14.81380 0.87287
+ 0.31416 14.85071 1.34688
+ 0.34558 14.89842 1.51588
+ 0.37699 14.94596 1.30661
+ 0.40841 14.98052 0.68187
+ 0.43982 14.98880 -0.32791
+ 0.47124 14.95992 -1.69025
+ 0.50265 14.88260 -3.29052
+ 0.53407 14.75317 -4.96947
+ 0.56549 14.57036 -6.58050
+ 0.59690 14.33970 -7.94522
+ 0.62832 14.07115 -8.95276
+ 0.65973 13.77719 -9.54424
+ 0.69115 13.47147 -9.71559
+ 0.72257 13.16674 -9.52214
+ 0.75398 12.87318 -9.04455
+ 0.78540 12.59845 -8.35746
+ 0.81681 12.34806 -7.53288
+ 0.84823 12.12515 -6.63737
+ 0.87965 11.93102 -5.70555
+ 0.91106 11.76666 -4.77067
+ 0.94248 11.63127 -3.85511
+ 0.97389 11.52443 -2.96150
+ 1.00531 11.44519 -2.10886
+ 1.03673 11.39193 -1.30973
+ 1.06814 11.36290 -0.57795
+ 1.09956 11.35562 0.06564
+ 1.13097 11.36702 0.60908
+ 1.16239 11.39388 1.04956
+ 1.19381 11.43297 1.39725
+ 1.22522 11.48168 1.67383
+ 1.25664 11.53814 1.91235
+ 1.28805 11.60183 2.15400
+ 1.31947 11.67348 2.43040
+ 1.35088 11.75454 2.78076
+ 1.38230 11.84820 3.21639
+ 1.41372 11.95663 3.73112
+ 1.44513 12.08264 4.31252
+ 1.47655 12.22760 4.93997
+ 1.50796 12.39302 5.59522
+ 1.53938 12.57915 6.22538
+ 1.57080 12.78417 6.81465
+ 1.60221 13.00733 7.31439
+ 1.63363 13.24375 7.69216
+ 1.66504 13.49064 7.92523
+ 1.69646 13.74171 7.96631
+ 1.72788 13.99118 7.82705
+ 1.75929 14.23350 7.52661
+ 1.79071 14.46409 7.07963
+ 1.82212 14.67832 6.56183
+ 1.85354 14.87639 6.02293
+ 1.88496 15.05676 5.48870
+ 1.91637 15.22125 4.97648
+ 1.94779 15.36943 4.47050
+ 1.97920 15.50214 3.93312
+ 2.01062 15.61656 3.25777
+ 2.04203 15.70683 2.41601
+ 2.07345 15.76836 1.35324
+ 2.10487 15.79186 0.07937
+ 2.13628 15.77335 -1.32078
+ 2.16770 15.70887 -2.78132
+ 2.19911 15.59859 -4.15591
+ 2.23053 15.44775 -5.35838
+ 2.26195 15.26192 -6.29576
+ 2.29336 15.05217 -6.91512
+ 2.32478 14.82742 -7.29068
+ 2.35619 14.59409 -7.47898
+ 2.38761 14.35751 -7.52943
+ 2.41903 14.12100 -7.53571
+ 2.45044 13.88403 -7.59844
+ 2.48186 13.64358 -7.73822
+ 2.51327 13.39782 -7.97864
+ 2.54469 13.14226 -8.41694
+ 2.57611 12.86897 -9.08704
+ 2.60752 12.57131 -9.95794
+ 2.63894 12.24329 -11.01270
+ 2.67035 11.87936 -12.16703
+ 2.70177 11.47881 -13.30580
+ 2.73319 11.04332 -14.32339
+ 2.76460 10.57884 -15.12139
+ 2.79602 10.09323 -15.64548
+ 2.82743 9.59582 -15.88386
+ 2.85885 9.09522 -15.86574
+ 2.89026 8.59895 -15.63372
+ 2.92168 8.11292 -15.24911
+ 2.95310 7.64082 -14.77260
+ 2.98451 7.18473 -14.26221
+ 3.01593 6.74469 -13.77231
+ 3.04734 6.31939 -13.34976
+ 3.07876 5.90590 -13.02634
+ 3.11018 5.50091 -12.81419
diff --git a/regtest/basic/rt65/trajectory.xyz b/regtest/basic/rt65/trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..efd55fc9798338c494ff980f338bdc8bdf9748ad
--- /dev/null
+++ b/regtest/basic/rt65/trajectory.xyz
@@ -0,0 +1,670 @@
+65
+ generated by VMD
+ H5T 14.847420 1.772776 4.201096
+ O5' 14.896201 1.694230 4.226919
+ C5' 14.992702 1.713513 4.336967
+ 1H5' 15.043725 1.617648 4.346333
+ 2H5' 14.931581 1.744887 4.421588
+ C4' 15.109325 1.815422 4.313169
+ H4' 15.187816 1.806181 4.388236
+ O4' 15.167566 1.808275 4.180243
+ C1' 15.187524 1.937432 4.125737
+ H1' 15.288992 1.958157 4.091741
+ N9 15.113276 1.952933 3.995719
+ C8 15.022908 1.873954 3.928178
+ H8 14.982371 1.781079 3.965527
+ N7 14.971737 1.930705 3.820266
+ C5 15.029648 2.053877 3.819370
+ C6 15.025768 2.167929 3.734162
+ N6 14.939121 2.182113 3.633917
+ H61 14.914086 2.100017 3.580677
+ H62 14.937536 2.270351 3.584798
+ N1 15.103413 2.275954 3.754111
+ C2 15.182701 2.273724 3.855718
+ H2 15.259680 2.349052 3.863716
+ N3 15.187340 2.182850 3.952467
+ C4 15.120228 2.070090 3.922029
+ C3' 15.035816 1.958286 4.311849
+ H3' 14.939285 1.948002 4.262280
+ C2' 15.148665 2.036268 4.234992
+ 1H2' 15.110026 2.132472 4.201334
+ O2' 15.260274 2.057905 4.323319
+ 2HO' 15.230085 2.128216 4.381293
+ O3' 15.023906 1.998978 4.444931
+ P 14.882421 2.034298 4.503669
+ O1P 14.885519 2.029100 4.653514
+ O2P 14.778923 1.947499 4.435366
+ O5' 14.872825 2.189016 4.459605
+ C5' 14.940541 2.299417 4.518781
+ 1H5' 15.049508 2.297146 4.517267
+ 2H5' 14.923553 2.312758 4.625619
+ C4' 14.913382 2.437655 4.441618
+ H4' 14.960114 2.516044 4.501219
+ O4' 14.991676 2.446961 4.318547
+ C1' 14.894224 2.496199 4.223132
+ H1' 14.937422 2.573962 4.160140
+ N9 14.843146 2.395506 4.128749
+ C8 14.852216 2.257627 4.142356
+ H8 14.904563 2.207837 4.222633
+ N7 14.785973 2.194726 4.048380
+ C5 14.742547 2.293209 3.962341
+ C6 14.664241 2.302546 3.850103
+ N6 14.625215 2.203424 3.779305
+ H61 14.641452 2.107252 3.805538
+ H62 14.581784 2.236622 3.694378
+ N1 14.626487 2.422118 3.794508
+ C2 14.678065 2.530943 3.851064
+ H2 14.648037 2.626358 3.810341
+ N3 14.751561 2.538620 3.962151
+ C4 14.777925 2.415613 4.010852
+ C3' 14.765208 2.460481 4.413977
+ H3' 14.716369 2.371144 4.375062
+ C2' 14.776618 2.561126 4.300804
+ 1H2' 14.684395 2.563750 4.242760
+ O2' 14.824705 2.695651 4.325369
+ 2HO' 14.799959 2.754887 4.253991
+ O3' 14.698467 2.513825 4.521744
+ H3T 14.609154 2.545954 4.507367
+65
+ generated by VMD
+ H5T 14.797546 1.832525 4.381888
+ O5' 14.806289 1.752446 4.329672
+ C5' 14.901293 1.757977 4.228772
+ 1H5' 14.866888 1.819771 4.145833
+ 2H5' 14.918494 1.657468 4.190259
+ C4' 15.033164 1.817925 4.277514
+ H4' 15.069221 1.754881 4.358793
+ O4' 15.126022 1.812059 4.162668
+ C1' 15.183326 1.943732 4.138662
+ H1' 15.291444 1.942941 4.124839
+ N9 15.113312 2.005918 4.016412
+ C8 15.045125 1.944269 3.916965
+ H8 15.032977 1.837563 3.928374
+ N7 14.988688 2.016555 3.824484
+ C5 15.039663 2.141150 3.857107
+ C6 15.037766 2.266198 3.798166
+ N6 14.971131 2.300894 3.689602
+ H61 14.896909 2.239116 3.660015
+ H62 14.976900 2.397799 3.661726
+ N1 15.099638 2.373748 3.845444
+ C2 15.175701 2.353911 3.952780
+ H2 15.221227 2.444624 3.989691
+ N3 15.194207 2.237123 4.019596
+ C4 15.114303 2.136575 3.968732
+ C3' 15.035360 1.964626 4.320169
+ H3' 14.954812 2.020132 4.272085
+ C2' 15.161895 2.026635 4.264152
+ 1H2' 15.151196 2.132333 4.239770
+ O2' 15.274509 1.995500 4.336793
+ 2HO' 15.286169 2.077091 4.386017
+ O3' 15.036485 1.982491 4.461981
+ P 14.913964 2.036578 4.537579
+ O1P 14.941110 2.042828 4.677788
+ O2P 14.806670 1.942226 4.497838
+ O5' 14.878706 2.181873 4.480193
+ C5' 14.973777 2.282000 4.497470
+ 1H5' 15.074605 2.240984 4.491771
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+ C4' 14.960764 2.394531 4.390433
+ H4' 15.028895 2.476485 4.413289
+ O4' 14.989053 2.357359 4.260358
+ C1' 14.904777 2.425674 4.175336
+ H1' 14.968537 2.474184 4.101429
+ N9 14.813373 2.335255 4.105164
+ C8 14.774955 2.208137 4.129881
+ H8 14.794060 2.151025 4.219532
+ N7 14.713981 2.147487 4.031319
+ C5 14.708177 2.242913 3.936696
+ C6 14.646914 2.245469 3.808760
+ N6 14.571647 2.156780 3.749764
+ H61 14.542524 2.073044 3.798148
+ H62 14.520075 2.188365 3.668870
+ N1 14.641324 2.362669 3.741292
+ C2 14.701813 2.466049 3.798936
+ H2 14.706003 2.556145 3.739528
+ N3 14.766210 2.474183 3.914001
+ C4 14.754867 2.359369 3.985221
+ C3' 14.813626 2.453006 4.397973
+ H3' 14.738989 2.373738 4.392804
+ C2' 14.815772 2.521017 4.262980
+ 1H2' 14.713857 2.519253 4.224363
+ O2' 14.874209 2.646233 4.260289
+ 2HO' 14.833235 2.714067 4.314472
+ O3' 14.786455 2.538643 4.511051
+ H3T 14.695704 2.525192 4.539330
+65
+ generated by VMD
+ H5T 15.097142 1.668326 4.109947
+ O5' 15.046495 1.665248 4.191442
+ C5' 15.124683 1.723198 4.293117
+ 1H5' 15.228861 1.691790 4.299565
+ 2H5' 15.079405 1.705176 4.390616
+ C4' 15.129340 1.872468 4.275512
+ H4' 15.210347 1.907524 4.339464
+ O4' 15.177201 1.902492 4.148199
+ C1' 15.117216 2.023489 4.100878
+ H1' 15.194286 2.099443 4.087759
+ N9 15.043651 2.020701 3.973052
+ C8 14.951991 1.931444 3.935999
+ H8 14.914091 1.855570 4.002862
+ N7 14.922978 1.937139 3.812580
+ C5 15.002272 2.045211 3.763760
+ C6 15.012959 2.114496 3.641779
+ N6 14.968732 2.067341 3.526960
+ H61 14.917503 1.980394 3.531065
+ H62 15.008677 2.109936 3.444552
+ N1 15.095745 2.211320 3.623265
+ C2 15.165342 2.253631 3.734057
+ H2 15.232390 2.335036 3.710782
+ N3 15.165565 2.198909 3.857847
+ C4 15.074628 2.093823 3.866636
+ C3' 15.002029 1.945333 4.306546
+ H3' 14.916491 1.879201 4.292741
+ C2' 15.017333 2.071405 4.210642
+ 1H2' 14.918507 2.098437 4.173444
+ O2' 15.087488 2.175789 4.271819
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+ O3' 14.990348 1.980879 4.446596
+ P 14.857903 2.037183 4.513322
+ O1P 14.877825 2.029214 4.656148
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+ C5' 14.933087 2.285940 4.539681
+ 1H5' 15.038389 2.257839 4.541404
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+ C4' 14.931292 2.435342 4.486126
+ H4' 14.989725 2.502450 4.549078
+ O4' 14.968204 2.445903 4.352262
+ C1' 14.856408 2.502898 4.277845
+ H1' 14.897898 2.580996 4.214125
+ N9 14.795577 2.400006 4.190372
+ C8 14.714306 2.291367 4.222795
+ H8 14.663243 2.271842 4.315938
+ N7 14.668910 2.232421 4.112843
+ C5 14.746554 2.287563 4.010130
+ C6 14.754593 2.257437 3.872097
+ N6 14.685724 2.157914 3.813751
+ H61 14.630732 2.100684 3.876213
+ H62 14.707831 2.134947 3.717914
+ N1 14.837722 2.329980 3.800696
+ C2 14.913857 2.422629 3.854674
+ H2 14.974173 2.482054 3.787631
+ N3 14.916680 2.462957 3.981540
+ C4 14.825435 2.390300 4.058403
+ C3' 14.781671 2.480878 4.496495
+ H3' 14.724883 2.388146 4.488949
+ C2' 14.764706 2.572741 4.378519
+ 1H2' 14.664557 2.589872 4.339051
+ O2' 14.821342 2.697761 4.413458
+ 2HO' 14.797153 2.759951 4.344442
+ O3' 14.746025 2.547402 4.618172
+ H3T 14.761264 2.641381 4.605847
+65
+ generated by VMD
+ H5T 14.896517 1.722039 4.256091
+ O5' 14.974108 1.684743 4.213608
+ C5' 15.073586 1.678005 4.311006
+ 1H5' 15.153643 1.606393 4.292474
+ 2H5' 15.034431 1.655961 4.410314
+ C4' 15.144793 1.821773 4.321304
+ H4' 15.203806 1.826254 4.412838
+ O4' 15.215021 1.849773 4.200249
+ C1' 15.197684 1.988282 4.162799
+ H1' 15.298632 2.026277 4.147079
+ N9 15.109707 1.993706 4.034468
+ C8 15.059310 1.889387 3.965481
+ H8 15.045170 1.791467 4.008790
+ N7 15.010215 1.916534 3.847403
+ C5 15.035903 2.048973 3.829019
+ C6 15.011794 2.141888 3.726766
+ N6 14.947181 2.125660 3.618889
+ H61 14.891392 2.042211 3.607724
+ H62 14.907223 2.203487 3.568419
+ N1 15.041734 2.272362 3.741960
+ C2 15.094986 2.307462 3.863274
+ H2 15.129761 2.407641 3.883739
+ N3 15.128124 2.226311 3.965864
+ C4 15.096125 2.097537 3.941687
+ C3' 15.044984 1.935202 4.337620
+ H3' 14.957216 1.921462 4.274460
+ C2' 15.120823 2.054060 4.281669
+ 1H2' 15.057999 2.132215 4.238936
+ O2' 15.215878 2.101759 4.370345
+ 2HO' 15.190849 2.057137 4.451575
+ O3' 15.012177 1.959000 4.471820
+ P 14.865489 2.009048 4.514957
+ O1P 14.856316 2.014251 4.664734
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+ C5' 14.936448 2.263116 4.522058
+ 1H5' 15.043159 2.254232 4.542422
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+ C4' 14.933058 2.391823 4.437636
+ H4' 15.002481 2.461632 4.484410
+ O4' 14.965080 2.359071 4.306986
+ C1' 14.914851 2.449100 4.208991
+ H1' 14.991192 2.515312 4.168135
+ N9 14.842881 2.366482 4.105685
+ C8 14.784214 2.243840 4.124059
+ H8 14.818416 2.176592 4.201338
+ N7 14.701168 2.202450 4.028914
+ C5 14.690821 2.318115 3.943541
+ C6 14.620112 2.362557 3.829230
+ N6 14.531917 2.297515 3.759082
+ H61 14.494678 2.206164 3.780740
+ H62 14.508058 2.343673 3.672473
+ N1 14.654975 2.467176 3.760733
+ C2 14.757774 2.538561 3.802464
+ H2 14.788578 2.614861 3.732509
+ N3 14.823767 2.523345 3.918492
+ C4 14.781515 2.410989 3.989729
+ C3' 14.798530 2.466371 4.421867
+ H3' 14.713267 2.398849 4.414640
+ C2' 14.820069 2.541733 4.291849
+ 1H2' 14.721073 2.533303 4.247020
+ O2' 14.879740 2.668829 4.295744
+ 2HO' 14.853123 2.709278 4.212851
+ O3' 14.777799 2.564872 4.524009
+ H3T 14.774690 2.652156 4.484158
+65
+ generated by VMD
+ H5T 15.206599 1.572029 4.334027
+ O5' 15.143420 1.613157 4.393466
+ C5' 15.204591 1.721485 4.460211
+ 1H5' 15.302390 1.686471 4.493228
+ 2H5' 15.145994 1.749638 4.547704
+ C4' 15.222277 1.839862 4.366666
+ H4' 15.296083 1.905875 4.412229
+ O4' 15.274338 1.807258 4.236629
+ C1' 15.236064 1.914908 4.149570
+ H1' 15.330606 1.960101 4.119559
+ N9 15.180844 1.859583 4.024785
+ C8 15.061384 1.800116 3.998049
+ H8 14.979607 1.784122 4.066754
+ N7 15.068254 1.739242 3.884995
+ C5 15.188682 1.768900 3.825654
+ C6 15.254227 1.730517 3.714267
+ N6 15.197144 1.668724 3.611931
+ H61 15.097814 1.651520 3.618143
+ H62 15.253335 1.657661 3.528737
+ N1 15.380466 1.758555 3.696045
+ C2 15.438334 1.837651 3.782535
+ H2 15.538693 1.860716 3.749975
+ N3 15.386237 1.887903 3.893170
+ C4 15.259776 1.848152 3.907741
+ C3' 15.095292 1.915299 4.334499
+ H3' 15.010189 1.854632 4.303551
+ C2' 15.135535 2.008978 4.223885
+ 1H2' 15.057730 2.028799 4.150165
+ O2' 15.213609 2.121090 4.267405
+ 2HO' 15.162492 2.179283 4.324121
+ O3' 15.074284 1.989543 4.453595
+ P 14.952164 2.082008 4.470041
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+ C5' 14.892916 2.333297 4.425739
+ 1H5' 14.942754 2.425604 4.396129
+ 2H5' 14.868936 2.344323 4.531496
+ C4' 14.762017 2.328242 4.346614
+ H4' 14.687031 2.274320 4.404495
+ O4' 14.715004 2.463836 4.325877
+ C1' 14.642533 2.468390 4.202215
+ H1' 14.537689 2.456767 4.229668
+ N9 14.660139 2.595785 4.130150
+ C8 14.765982 2.642884 4.050838
+ H8 14.863976 2.597805 4.045431
+ N7 14.742874 2.750244 3.983194
+ C5 14.609942 2.788411 4.021593
+ C6 14.530947 2.904861 4.004297
+ N6 14.577147 3.017766 3.945367
+ H61 14.671611 3.011784 3.910125
+ H62 14.516243 3.094875 3.922008
+ N1 14.402965 2.905596 4.044899
+ C2 14.356116 2.800324 4.114378
+ H2 14.253911 2.798593 4.149237
+ N3 14.422529 2.684535 4.147936
+ C4 14.554123 2.689645 4.097775
+ C3' 14.759785 2.258157 4.211955
+ H3' 14.862022 2.244558 4.176696
+ C2' 14.688461 2.351718 4.114935
+ 1H2' 14.758523 2.390571 4.041025
+ O2' 14.583876 2.283096 4.050872
+ 2HO' 14.579090 2.200263 4.099160
+ O3' 14.699176 2.129625 4.228271
+ H3T 14.759976 2.086417 4.288707
+65
+ generated by VMD
+ H5T 14.837190 1.731764 4.112862
+ O5' 14.835567 1.749919 4.207116
+ C5' 14.955059 1.709752 4.264459
+ 1H5' 14.994122 1.636536 4.193788
+ 2H5' 14.941088 1.676506 4.367320
+ C4' 15.058025 1.817933 4.264746
+ H4' 15.131132 1.773256 4.332129
+ O4' 15.109529 1.845337 4.136002
+ C1' 15.138430 1.984277 4.128410
+ H1' 15.244407 1.999515 4.107976
+ N9 15.070132 2.041045 4.008841
+ C8 14.990027 1.973175 3.921563
+ H8 14.971063 1.869021 3.942928
+ N7 14.973977 2.028135 3.807398
+ C5 15.029313 2.159239 3.827452
+ C6 15.046778 2.267987 3.746533
+ N6 15.005386 2.286913 3.620339
+ H61 14.965146 2.209908 3.568843
+ H62 15.012429 2.378862 3.579145
+ N1 15.107679 2.380051 3.796883
+ C2 15.159229 2.371572 3.920658
+ H2 15.206707 2.461028 3.958174
+ N3 15.163549 2.271095 4.005847
+ C4 15.083906 2.169787 3.953650
+ C3' 15.001925 1.947165 4.323164
+ H3' 14.907749 1.969282 4.272937
+ C2' 15.103126 2.048822 4.258628
+ 1H2' 15.061421 2.148594 4.244948
+ O2' 15.219626 2.062929 4.344001
+ 2HO' 15.204728 1.999661 4.414649
+ O3' 14.985111 1.958341 4.462287
+ P 14.870660 2.053093 4.523168
+ O1P 14.890329 2.040473 4.667353
+ O2P 14.740082 2.006428 4.468818
+ O5' 14.879867 2.213993 4.478765
+ C5' 15.000712 2.295078 4.505804
+ 1H5' 15.093207 2.240039 4.488584
+ 2H5' 15.007841 2.320825 4.611480
+ C4' 15.016975 2.416266 4.416747
+ H4' 15.119471 2.451387 4.428679
+ O4' 15.012310 2.368953 4.283223
+ C1' 14.885431 2.408447 4.231414
+ H1' 14.909578 2.486356 4.159110
+ N9 14.828690 2.302046 4.146806
+ C8 14.770106 2.182823 4.181708
+ H8 14.763678 2.144738 4.282567
+ N7 14.724207 2.113139 4.078411
+ C5 14.738846 2.199121 3.968082
+ C6 14.685157 2.199994 3.839454
+ N6 14.641347 2.088488 3.783013
+ H61 14.630588 2.003700 3.836828
+ H62 14.617175 2.091475 3.684993
+ N1 14.685962 2.312217 3.769986
+ C2 14.738795 2.421787 3.819924
+ H2 14.743470 2.510610 3.758665
+ N3 14.788108 2.434139 3.945859
+ C4 14.788066 2.318882 4.016373
+ C3' 14.902862 2.517875 4.438258
+ H3' 14.862687 2.518752 4.539581
+ C2' 14.798081 2.468604 4.336346
+ 1H2' 14.725121 2.396255 4.372725
+ O2' 14.722972 2.571498 4.275081
+ 2HO' 14.634643 2.551233 4.306754
+ O3' 14.944068 2.643189 4.387441
+ H3T 14.875720 2.667839 4.324697
+65
+ generated by VMD
+ H5T 15.025169 1.552304 4.239150
+ O5' 15.015182 1.647334 4.248394
+ C5' 15.141973 1.709659 4.291545
+ 1H5' 15.226773 1.672057 4.234307
+ 2H5' 15.151942 1.692474 4.398718
+ C4' 15.149358 1.861311 4.269546
+ H4' 15.244267 1.898158 4.308477
+ O4' 15.161581 1.876086 4.133709
+ C1' 15.109478 2.011050 4.104973
+ H1' 15.190284 2.083412 4.115696
+ N9 15.053378 2.010486 3.974542
+ C8 14.949608 1.939907 3.926584
+ H8 14.888913 1.876979 3.989987
+ N7 14.924644 1.959011 3.802988
+ C5 15.020497 2.055530 3.767023
+ C6 15.033942 2.135434 3.652987
+ N6 14.963105 2.128827 3.540459
+ H61 14.895276 2.054775 3.529661
+ H62 14.982648 2.205026 3.477112
+ N1 15.124428 2.225896 3.646025
+ C2 15.208601 2.243128 3.748986
+ H2 15.282596 2.319057 3.728404
+ N3 15.205704 2.173504 3.865497
+ C4 15.105607 2.076787 3.868620
+ C3' 15.021268 1.940332 4.306942
+ H3' 14.940172 1.869729 4.289064
+ C2' 15.014707 2.060263 4.211948
+ 1H2' 14.914454 2.080501 4.174254
+ O2' 15.075030 2.181257 4.269489
+ 2HO' 15.030182 2.202334 4.351711
+ O3' 15.009482 1.974985 4.448845
+ P 14.874564 2.036387 4.506008
+ O1P 14.874916 2.025261 4.649406
+ O2P 14.763107 1.972056 4.434628
+ O5' 14.872576 2.186512 4.459989
+ C5' 14.934460 2.285841 4.539440
+ 1H5' 15.041437 2.264965 4.540383
+ 2H5' 14.903284 2.279682 4.643705
+ C4' 14.913041 2.433059 4.492862
+ H4' 14.969533 2.501193 4.556480
+ O4' 14.958048 2.439136 4.359442
+ C1' 14.860572 2.499717 4.269575
+ H1' 14.896607 2.576455 4.201065
+ N9 14.789545 2.409343 4.182176
+ C8 14.689377 2.324483 4.217869
+ H8 14.648006 2.309146 4.316444
+ N7 14.635345 2.260870 4.122424
+ C5 14.720469 2.293509 4.015628
+ C6 14.723079 2.253921 3.878083
+ N6 14.635610 2.177386 3.811405
+ H61 14.557884 2.135336 3.860309
+ H62 14.657583 2.147101 3.717592
+ N1 14.824955 2.302587 3.803629
+ C2 14.915488 2.387402 3.852718
+ H2 14.992708 2.423151 3.786211
+ N3 14.912703 2.441381 3.973917
+ C4 14.813445 2.387689 4.050976
+ C3' 14.766768 2.486320 4.491781
+ H3' 14.692776 2.406437 4.486772
+ C2' 14.760048 2.572060 4.368409
+ 1H2' 14.659533 2.583792 4.327912
+ O2' 14.821878 2.698505 4.390593
+ 2HO' 14.758530 2.751030 4.440028
+ O3' 14.742419 2.565792 4.609941
+ H3T 14.715851 2.655730 4.589423
+65
+ generated by VMD
+ H5T 15.179457 1.741104 3.900982
+ O5' 15.103093 1.777243 3.855390
+ C5' 14.987530 1.777926 3.937434
+ 1H5' 14.967832 1.672874 3.958816
+ 2H5' 14.901471 1.825049 3.889954
+ C4' 15.013573 1.864984 4.067422
+ H4' 14.926151 1.861565 4.132435
+ O4' 15.123556 1.807494 4.143685
+ C1' 15.224981 1.903663 4.148447
+ H1' 15.223179 1.944826 4.249360
+ N9 15.361039 1.850121 4.127141
+ C8 15.475318 1.881727 4.191302
+ H8 15.491652 1.957671 4.266335
+ N7 15.580411 1.809070 4.159493
+ C5 15.525576 1.719523 4.067212
+ C6 15.583897 1.619220 3.989246
+ N6 15.711239 1.582531 3.994646
+ H61 15.773693 1.628168 4.059591
+ H62 15.740669 1.513267 3.927286
+ N1 15.511261 1.544478 3.904103
+ C2 15.380339 1.574850 3.909242
+ H2 15.319757 1.529302 3.832304
+ N3 15.313910 1.665238 3.979821
+ C4 15.392190 1.739197 4.052656
+ C3' 15.048454 2.010539 4.040118
+ H3' 15.015978 2.034432 3.938848
+ C2' 15.203575 2.009545 4.043818
+ 1H2' 15.250134 1.981461 3.949349
+ O2' 15.259817 2.131708 4.089610
+ 2HO' 15.228335 2.194728 4.024391
+ O3' 14.996343 2.096307 4.138817
+ P 14.842931 2.132808 4.145224
+ O1P 14.781137 2.038660 4.245789
+ O2P 14.795316 2.136425 4.007238
+ O5' 14.834799 2.286782 4.197085
+ C5' 14.907822 2.391318 4.137965
+ 1H5' 14.892282 2.382674 4.030425
+ 2H5' 15.012506 2.374146 4.163009
+ C4' 14.869848 2.528366 4.193048
+ H4' 14.926466 2.612052 4.152155
+ O4' 14.729959 2.550426 4.171509
+ C1' 14.672099 2.600095 4.289897
+ H1' 14.700438 2.705135 4.296573
+ N9 14.528367 2.588774 4.285998
+ C8 14.441617 2.523839 4.366195
+ H8 14.480587 2.475313 4.454459
+ N7 14.320478 2.508995 4.321265
+ C5 14.317728 2.592256 4.210869
+ C6 14.226738 2.642013 4.115617
+ N6 14.100051 2.607729 4.115785
+ H61 14.057688 2.563380 4.196032
+ H62 14.040026 2.665291 4.058475
+ N1 14.257448 2.722378 4.012711
+ C2 14.384749 2.753088 4.002584
+ H2 14.405425 2.821341 3.921478
+ N3 14.485984 2.723563 4.081551
+ C4 14.445708 2.637608 4.183837
+ C3' 14.897259 2.523561 4.344881
+ H3' 14.964549 2.443965 4.376780
+ C2' 14.751207 2.530166 4.402293
+ 1H2' 14.724064 2.428333 4.430120
+ O2' 14.738544 2.621317 4.511948
+ 2HO' 14.752827 2.572472 4.593349
+ O3' 14.964114 2.644466 4.377091
+ H3T 14.943527 2.658123 4.469858
+65
+ generated by VMD
+ H5T 14.654305 2.132374 4.221466
+ O5' 14.740575 2.107329 4.187611
+ C5' 14.770223 2.001941 4.275386
+ 1H5' 14.682770 1.936934 4.272764
+ 2H5' 14.775343 2.049791 4.373187
+ C4' 14.906325 1.926109 4.267467
+ H4' 14.921304 1.854206 4.348008
+ O4' 14.918378 1.855741 4.144278
+ C1' 15.050409 1.869009 4.097060
+ H1' 15.093917 1.772598 4.070735
+ N9 15.063756 1.958524 3.977970
+ C8 15.001014 2.077048 3.948780
+ H8 14.921307 2.113573 4.011842
+ N7 15.042750 2.133699 3.837873
+ C5 15.134868 2.046790 3.789779
+ C6 15.219357 2.042315 3.676820
+ N6 15.225701 2.128914 3.585231
+ H61 15.156734 2.202191 3.576563
+ H62 15.292335 2.109260 3.511917
+ N1 15.294324 1.944477 3.643432
+ C2 15.297135 1.842909 3.730301
+ H2 15.361707 1.759751 3.706231
+ N3 15.216388 1.823233 3.833624
+ C4 15.141820 1.932562 3.862231
+ C3' 15.032075 2.018549 4.281206
+ H3' 15.013633 2.109337 4.223773
+ C2' 15.133450 1.922012 4.208516
+ 1H2' 15.215766 1.981275 4.168603
+ O2' 15.173163 1.811780 4.291770
+ 2HO' 15.207495 1.851636 4.372073
+ O3' 15.071229 2.043559 4.415228
+ P 15.125263 2.184964 4.445612
+ O1P 15.223106 2.221821 4.341271
+ O2P 15.170097 2.177119 4.584393
+ O5' 15.002633 2.280640 4.437276
+ C5' 14.952951 2.352589 4.547473
+ 1H5' 15.029819 2.424535 4.575695
+ 2H5' 14.940403 2.287287 4.633840
+ C4' 14.815311 2.421970 4.523385
+ H4' 14.772344 2.452369 4.618835
+ O4' 14.831726 2.525931 4.423570
+ C1' 14.726851 2.517488 4.325172
+ H1' 14.695997 2.613786 4.284483
+ N9 14.776684 2.453874 4.202466
+ C8 14.905722 2.422574 4.163041
+ H8 14.991037 2.433325 4.228383
+ N7 14.913260 2.383031 4.039737
+ C5 14.784368 2.388160 3.988065
+ C6 14.729931 2.366491 3.860029
+ N6 14.796456 2.313958 3.757921
+ H61 14.894579 2.291887 3.767181
+ H62 14.755410 2.300120 3.666680
+ N1 14.598265 2.362259 3.847806
+ C2 14.523367 2.396977 3.956361
+ H2 14.417350 2.381791 3.942446
+ N3 14.564178 2.428225 4.081981
+ C4 14.701248 2.426260 4.089754
+ C3' 14.712963 2.332113 4.464497
+ H3' 14.761755 2.268072 4.391019
+ C2' 14.620694 2.431362 4.389987
+ 1H2' 14.553188 2.380996 4.320798
+ O2' 14.547445 2.516590 4.477498
+ 2HO' 14.519221 2.460116 4.549816
+ O3' 14.634567 2.259115 4.558148
+ H3T 14.678012 2.177521 4.584057
+65
+ generated by VMD
+ H5T 15.139706 1.691906 4.119927
+ O5' 15.097111 1.703936 4.205115
+ C5' 15.182992 1.776412 4.292105
+ 1H5' 15.282006 1.732136 4.281291
+ 2H5' 15.149679 1.767901 4.395540
+ C4' 15.173301 1.924599 4.260819
+ H4' 15.238002 1.964472 4.338953
+ O4' 15.213679 1.971138 4.134460
+ C1' 15.118810 2.055132 4.090411
+ H1' 15.163068 2.148366 4.055342
+ N9 15.047133 1.996337 3.972012
+ C8 14.963219 1.891788 3.962123
+ H8 14.930859 1.835465 4.048404
+ N7 14.912887 1.878921 3.839806
+ C5 14.975141 1.974246 3.759592
+ C6 14.970608 2.020350 3.629150
+ N6 14.887928 1.976898 3.538360
+ H61 14.811019 1.915833 3.561963
+ H62 14.880107 2.045012 3.464197
+ N1 15.039798 2.126328 3.587474
+ C2 15.129487 2.187153 3.672333
+ H2 15.185096 2.274561 3.641810
+ N3 15.133538 2.158725 3.803795
+ C4 15.056976 2.051141 3.842332
+ C3' 15.024463 1.968347 4.283900
+ H3' 14.957707 1.886816 4.256019
+ C2' 15.016562 2.087369 4.195502
+ 1H2' 14.919801 2.080824 4.145750
+ O2' 15.053941 2.213798 4.260862
+ 2HO' 14.991995 2.230488 4.332276
+ O3' 14.996555 1.997096 4.419310
+ P 14.848988 2.026661 4.468812
+ O1P 14.836275 1.998193 4.610259
+ O2P 14.759477 1.970746 4.369563
+ O5' 14.839829 2.182147 4.456972
+ C5' 14.883589 2.262748 4.560537
+ 1H5' 14.984632 2.226203 4.578864
+ 2H5' 14.829399 2.234568 4.650816
+ C4' 14.886683 2.416690 4.528798
+ H4' 14.948374 2.475328 4.596890
+ O4' 14.945946 2.432028 4.398474
+ C1' 14.859962 2.510331 4.322206
+ H1' 14.907434 2.588217 4.262530
+ N9 14.813416 2.427613 4.213445
+ C8 14.712191 2.333448 4.227327
+ H8 14.662790 2.314531 4.321485
+ N7 14.679394 2.270390 4.110848
+ C5 14.779932 2.319226 4.024812
+ C6 14.808763 2.289957 3.889882
+ N6 14.743375 2.197997 3.810560
+ H61 14.666928 2.145288 3.850301
+ H62 14.783525 2.182019 3.719271
+ N1 14.899675 2.363994 3.823681
+ C2 14.970441 2.454097 3.887055
+ H2 15.029579 2.520691 3.825966
+ N3 14.955811 2.482905 4.016510
+ C4 14.860398 2.414614 4.081480
+ C3' 14.742235 2.481310 4.524706
+ H3' 14.664103 2.407829 4.505290
+ C2' 14.754819 2.576566 4.405489
+ 1H2' 14.659711 2.576680 4.352241
+ O2' 14.789527 2.710984 4.440497
+ 2HO' 14.723193 2.741502 4.502822
+ O3' 14.725138 2.567655 4.638644
+ H3T 14.673618 2.525369 4.707736
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 8dd996c774d3b130fc71b2e2bfcd7b715168f60d..972f62b143fc8ad6b631fffe8faf82b2b1cc26c8 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -260,6 +260,51 @@ factor that can then be used to determine the rate. This method can be used toge
with \ref COMMITTOR analysis to stop the simulation when the system get to the target basin.
It must be used together with Well-Tempered Metadynamics.
+\par
+You can also provide a target distribution using the keyword TARGET
+\cite white2015designing
+\cite marinelli2015ensemble
+\cite gil2016empirical
+The TARGET should be a grid containing a free-energy (i.e. the -kbT*log of the desired target distribution).
+Gaussians will then be scaled by a factor
+\f[
+e^{\beta(\tilde{F}(s)-\tilde{F}_{max})}
+\f]
+Here \f$\tilde{F}(s)\f$ is the free energy defined on the grid and \f$\tilde{F}_{max}\f$ its maximum value.
+Notice that we here used the maximum value as in ref \cite gil2016empirical
+This choice allows to avoid exceedingly large Gaussians to be added. However,
+it could make the Gaussian too small. You should always choose carefully the HEIGHT parameter
+in this case.
+The grid file should be similar to other PLUMED grid files in that it should contain
+both the target free-energy and its derivatives.
+
+Notice that if you wish your simulation to converge to the target free energy you should use
+the DAMPFACTOR command to provide a global tempering \cite dama2014well
+Alternatively, if you use a BIASFACTOR yout simulation will converge to a free
+energy that is a linear combination of the target free energy and of the intrinsic free energy
+determined by the original force field.
+
+\verbatim
+DISTANCE ATOMS=3,5 LABEL=d1
+METAD ...
+ LABEL=t1
+ ARG=d1 SIGMA=0.05 TAU=200 DAMPFACTOR=100 PACE=250
+ GRID_MIN=0 GRID_MAX=2 GRID_BIN=200
+ TARGET=dist.dat
+... METAD
+
+PRINT ARG=d1,t1.bias STRIDE=100 FILE=COLVAR
+\endverbatim
+
+The header in the file dist.dat for this calculation would read:
+
+\verbatim
+#! FIELDS d1 t1.target der_d1
+#! SET min_d1 0
+#! SET max_d1 2
+#! SET nbins_d1 200
+#! SET periodic_d1 false
+\endverbatim
*/
//+ENDPLUMEDOC
@@ -291,6 +336,9 @@ private:
bool grid_;
double height0_;
double biasf_;
+ double dampfactor_;
+ std::string targetfilename_;
+ Grid* TargetGrid_;
double kbt_;
int stride_;
bool welltemp_;
@@ -354,9 +402,11 @@ void MetaD::registerKeywords(Keywords& keys){
keys.add("compulsory","SIGMA","the widths of the Gaussian hills");
keys.add("compulsory","PACE","the frequency for hill addition");
keys.add("compulsory","FILE","HILLS","a file in which the list of added hills is stored");
- keys.add("optional","HEIGHT","the heights of the Gaussian hills. Compulsory unless TAU, TEMP and BIASFACTOR are given");
+ keys.add("optional","HEIGHT","the heights of the Gaussian hills. Compulsory unless TAU and either BIASFACTOR or DAMPFACTOR are given");
keys.add("optional","FMT","specify format for HILLS files (useful for decrease the number of digits in regtests)");
keys.add("optional","BIASFACTOR","use well tempered metadynamics and use this biasfactor. Please note you must also specify temp");
+ keys.add("optional","DAMPFACTOR","damp hills with exp(-max(V)/(kbT*DAMPFACTOR)");
+ keys.add("optional","TARGET","target to a predefined distribution");
keys.add("optional","TEMP","the system temperature - this is only needed if you are doing well-tempered metadynamics");
keys.add("optional","TAU","in well tempered metadynamics, sets height to (kb*DeltaT*pace*timestep)/tau");
keys.add("optional","GRID_MIN","the lower bounds for the grid");
@@ -393,6 +443,7 @@ void MetaD::registerKeywords(Keywords& keys){
MetaD::~MetaD(){
if(flexbin) delete flexbin;
if(BiasGrid_) delete BiasGrid_;
+ if(TargetGrid_) delete TargetGrid_;
hillsOfile_.close();
if(wgridstride_>0) gridfile_.close();
delete [] dp_;
@@ -408,7 +459,8 @@ PLUMED_BIAS_INIT(ao),
// Grid stuff initialization
BiasGrid_(NULL), wgridstride_(0), grid_(false),
// Metadynamics basic parameters
-height0_(std::numeric_limits<double>::max()), biasf_(1.0), kbt_(0.0),
+height0_(std::numeric_limits<double>::max()), biasf_(1.0), dampfactor_(0.0), TargetGrid_(NULL),
+kbt_(0.0),
stride_(0), welltemp_(false),
// Other stuff
dp_(NULL), adaptive_(FlexibleBin::none),
@@ -486,6 +538,7 @@ last_step_warn_grid(0)
parse("FILE",hillsfname);
parse("BIASFACTOR",biasf_);
if( biasf_<1.0 ) error("well tempered bias factor is nonsensical");
+ parse("DAMPFACTOR",dampfactor_);
double temp=0.0;
parse("TEMP",temp);
if(temp>0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;
@@ -494,16 +547,23 @@ last_step_warn_grid(0)
if(kbt_==0.0) error("Unless the MD engine passes the temperature to plumed, with well-tempered metad you must specify it using TEMP");
welltemp_=true;
}
+ if(dampfactor_>0.0){
+ if(kbt_==0.0) error("Unless the MD engine passes the temperature to plumed, with damped metad you must specify it using TEMP");
+ }
+ parse("TARGET",targetfilename_);
+ if(targetfilename_.length()>0 && kbt_==0.0) error("with TARGET temperature must be specified");
double tau=0.0;
parse("TAU",tau);
if(tau==0.0){
if(height0_==std::numeric_limits<double>::max()) error("At least one between HEIGHT and TAU should be specified");
// if tau is not set, we compute it here from the other input parameters
if(welltemp_) tau=(kbt_*(biasf_-1.0))/height0_*getTimeStep()*stride_;
+ else if(dampfactor_>0.0) tau=(kbt_*dampfactor_)/height0_*getTimeStep()*stride_;
} else {
- if(!welltemp_)error("TAU only makes sense in well-tempered metadynamics");
if(height0_!=std::numeric_limits<double>::max()) error("At most one between HEIGHT and TAU should be specified");
- height0_=(kbt_*(biasf_-1.0))/tau*getTimeStep()*stride_;
+ if(welltemp_) height0_=(kbt_*(biasf_-1.0))/tau*getTimeStep()*stride_;
+ else if(dampfactor_>0.0) height0_=(kbt_*dampfactor_)/tau*getTimeStep()*stride_;
+ else error("TAU only makes sense in well-tempered or damped metadynamics");
}
// Grid Stuff
@@ -588,6 +648,9 @@ last_step_warn_grid(0)
if(adaptive_==FlexibleBin::diffusion || adaptive_==FlexibleBin::geometry) warning("reweighting has not been proven to work with adaptive Gaussians");
rewf_ustride_=50; parse("REWEIGHTING_NHILLS",rewf_ustride_);
}
+ if(dampfactor_>0.0){
+ if(!grid_) error("With DAMPFACTOR you should use grids");
+ }
// Multiple walkers
parse("WALKERS_N",mw_n_);
@@ -758,6 +821,16 @@ last_step_warn_grid(0)
// (e.g. in bias exchange with a neutral replica)
// see issue #168 on github
if(comm.Get_rank()==0 && walkers_mpi) multi_sim_comm.Barrier();
+ if(targetfilename_.length()>0){
+ IFile gridfile; gridfile.open(targetfilename_);
+ std::string funcl=getLabel() + ".target";
+ TargetGrid_=Grid::create(funcl,getArguments(),gridfile,false,false,true);
+ gridfile.close();
+ if(TargetGrid_->getDimension()!=getNumberOfArguments()) error("mismatch between dimensionality of input grid and number of arguments");
+ for(unsigned i=0;i<getNumberOfArguments();++i){
+ if( getPntrToArgument(i)->isPeriodic()!=TargetGrid_->getIsPeriodic()[i] ) error("periodicity mismatch between arguments and input bias");
+ }
+ }
// Calculate the Tiwary-Parrinello reweighting factor if we are restarting from previous hills
if(getRestart() && rewf_grid_.size()>0 ) computeReweightingFactor();
@@ -815,6 +888,11 @@ last_step_warn_grid(0)
"Pratyush and Parrinello, J. Phys. Chem. B, 119, 736 (2015)");
if(concurrent) log<<plumed.cite(
"Gil-Ley and Bussi, J. Chem. Theory Comput. 11, 1077 (2015)");
+ if(targetfilename_.length()>0){
+ log<<plumed.cite("White, Dama, and Voth, J. Chem. Theory Comput. 11, 2451 (2015)");
+ log<<plumed.cite("Marinelli and Faraldo-GoÌmez, Biophys. J. 108, 2779 (2015)");
+ log<<plumed.cite("Gil-Ley, Bottaro, and Bussi, submitted (2016)");
+ }
log<<"\n";
}
@@ -1139,6 +1217,15 @@ double MetaD::getHeight(const vector<double>& cv)
double vbias = getBiasAndDerivatives(cv);
height = height0_*exp(-vbias/(kbt_*(biasf_-1.0)));
}
+ if(dampfactor_>0.0){
+ plumed_assert(BiasGrid_);
+ double m=BiasGrid_->getMaxValue();
+ height*=exp(-m/(kbt_*(dampfactor_)));
+ }
+ if(TargetGrid_){
+ double f=TargetGrid_->getValue(cv)-TargetGrid_->getMaxValue();
+ height*=exp(f/kbt_);
+ }
return height;
}
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 0869142ea5e23e75c6da0994f74e7336c1a5724d..7925c274af3db66409268d88afb71ae3ede78e30 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -2197,3 +2197,46 @@ number = {11},
pages = {5062-5067},
year = {2015}
}
+
+@article{marinelli2015ensemble,
+ Author = {Marinelli, Fabrizio and Faraldo-G{\'o}mez, Jos{\'e} D},
+ Date-Added = {2015-07-24 14:22:59 +0000},
+ Date-Modified = {2015-09-27 11:05:20 +0000},
+ Journal = {Biophys. J.},
+ Number = {12},
+ Pages = {2779-2782},
+ Publisher = {Elsevier},
+ Title = {Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions},
+ Volume = {108},
+ Year = {2015}}
+
+@article{white2015designing,
+ Author = {White, Andrew and Dama, James and Voth, Gregory A},
+ Date-Added = {2015-07-24 14:23:23 +0000},
+ Date-Modified = {2015-09-27 11:08:36 +0000},
+ Journal = {J. Chem. Theory Comput.},
+ Number = {6},
+ Pages = {2451--2460},
+ Publisher = {ACS Publications},
+ Title = {Designing Free Energy Surfaces that Match Experimental Data with Metadynamics},
+ Volume = {11},
+ Year = {2015}}
+
+@article{dama2014well,
+ Author = {Dama, James F and Parrinello, Michele and Voth, Gregory A},
+ Journal = {Phys. Rev. Lett.},
+ Number = {24},
+ Pages = {240602},
+ Publisher = {APS},
+ Title = {Well-Tempered Metadynamics Converges Asymptotically},
+ Volume = {112},
+ Year = {2014}}
+
+
+@misc{gil2016empirical,
+ title={Empirical corrections to the Amber RNA force field with Target Metadynamics},
+ author={Gil-Ley, Alejandro and Bussi, Giovanni},
+ note={submitted}
+}
+
+