Merge branch 'v2.9' into v2.10

regtest/basic/rt-coverage-bias-type-2/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/basic/rt-coverage-bias-type-2/adenosine.pdb

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+TITLE     Protein in water
+REMARK    THIS IS A SIMULATION BOX
+CRYST1   29.788   29.788   29.788  70.53 109.47  70.53 P 1           1
+MODEL        1
+ATOM      1  O5'   A     1      29.350  26.420   9.100  1.00  0.00            
+ATOM      2  H5T   A     1      29.230  27.270   8.660  1.00  0.00            
+ATOM      3  C5'   A     1      30.060  26.570  10.350  1.00  0.00            
+ATOM      4 1H5'   A     1      30.970  27.120  10.120  1.00  0.00            
+ATOM      5 2H5'   A     1      30.390  25.620  10.780  1.00  0.00            
+ATOM      6  C4'   A     1      29.220  27.360  11.340  1.00  0.00            
+ATOM      7  H4'   A     1      29.860  27.720  12.140  1.00  0.00            
+ATOM      8  O4'   A     1      28.780  28.590  10.690  1.00  0.00            
+ATOM      9  C1'   A     1      27.340  28.670  10.650  1.00  0.00            
+ATOM     10  H1'   A     1      26.950  29.160  11.540  1.00  0.00            
+ATOM     11  N9    A     1      26.790  29.220   9.370  1.00  0.00            
+ATOM     12  C8    A     1      25.550  29.810   9.110  1.00  0.00            
+ATOM     13  H8    A     1      24.830  29.860   9.920  1.00  0.00            
+ATOM     14  N7    A     1      25.230  30.180   7.890  1.00  0.00            
+ATOM     15  C5    A     1      26.420  29.860   7.250  1.00  0.00            
+ATOM     16  C6    A     1      26.900  30.020   5.950  1.00  0.00            
+ATOM     17  N6    A     1      26.180  30.390   4.930  1.00  0.00            
+ATOM     18  H61   A     1      25.230  30.680   5.070  1.00  0.00            
+ATOM     19  H62   A     1      16.590   2.340   3.980  1.00  0.00            
+ATOM     20  N1    A     1      28.070  29.570   5.520  1.00  0.00            
+ATOM     21  C2    A     1      28.870  29.070   6.460  1.00  0.00            
+ATOM     22  H2    A     1      29.840  28.770   6.120  1.00  0.00            
+ATOM     23  N3    A     1      28.620  28.890   7.780  1.00  0.00            
+ATOM     24  C4    A     1      27.350  29.300   8.090  1.00  0.00            
+ATOM     25  C3'   A     1      28.010  26.690  11.870  1.00  0.00            
+ATOM     26  H3'   A     1      28.030  25.610  11.800  1.00  0.00            
+ATOM     27  C2'   A     1      26.990  27.200  10.850  1.00  0.00            
+ATOM     28 1H2'   A     1      27.030  26.670   9.900  1.00  0.00            
+ATOM     29  O2'   A     1      25.620  27.090  11.220  1.00  0.00            
+ATOM     30 2HO'   A     1      25.520  26.140  11.090  1.00  0.00            
+ATOM     31  O3'   A     1      27.570  27.090  13.220  1.00  0.00            
+ATOM     32  H3T   A     1      26.670  26.760  13.330  1.00  0.00            
+TER
+ENDMDL

regtest/basic/rt-coverage-bias-type-2/colvar.reference

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+#! FIELDS time j1 j2 j3 j4 j5 j6 j7
+ 0.000000   10.593    3.991    1.119    4.535    0.476    3.268    2.494
+ 10.000000    0.434    5.243    8.251    2.614    2.164    1.405    3.061
+ 20.000000    8.774    5.880    0.553    2.526    0.801    5.792    3.228
+ 30.000000   11.030    4.529    0.807    1.946    2.278    5.656    3.855
+ 40.000000   11.410    5.596    1.285    6.498    0.862    5.708    3.940
+ 50.000000   10.885    7.565    7.428    1.896    2.446    0.199    0.485
+ 60.000000    9.956    6.508    3.313    2.071    1.028    5.800    3.992
+ 70.000000   10.814    6.746    1.547    2.865    0.867    5.453    3.726
+ 80.000000    9.102    4.967    2.886    1.887    1.284    5.363    4.000
+ 90.000000    3.488    7.467    8.803    2.460    1.177    5.220    3.966
+ 100.000000    3.532    4.893   11.478    2.051    2.229    5.371    3.879

regtest/basic/rt-coverage-bias-type-2/config

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+type=driver
+arg="--plumed plumed.dat --mf_xtc traj.xtc --dump-forces forces --dump-forces-fmt=%8.2f"