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Commit 80cec6ce authored by Giovanni Bussi's avatar Giovanni Bussi
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Added regtest for fit-to-template

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regtest/basic/rt63c/Makefile 0 → 100644
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include ../../scripts/test.make
regtest/basic/rt63c/align.pdb 0 → 100644
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ATOM 1 HH31 ACE 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 HH31 ACE 1 1.000 0.000 0.000 1.00 0.00
ATOM 3 HH31 ACE 1 0.000 1.000 0.000 0.50 0.00
ATOM 3 HH31 ACE 1 0.000 1.000 0.000 0.50 0.00
ATOM 8 HH31 ACE 1 2.000 3.000 4.000 0.00 1.00
END
regtest/basic/rt63c/config 0 → 100644
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type=driver
arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial --dump-forces-fmt=%7.4f"
regtest/basic/rt63c/ddd.reference 0 → 100644
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#! FIELDS time aaaa aaaa2 rmsd rmsd2
0.000000 10.000000 10.000000 0.505276 0.505276
0.050000 10.000000 10.000000 0.586683 0.586683
0.100000 10.000000 10.000000 0.547766 0.547766
0.150000 10.000000 10.000000 0.711042 0.711042
0.200000 10.000000 10.000000 0.731741 0.731741
0.250000 10.000000 10.000000 0.458276 0.458276
0.300000 10.000000 10.000000 0.745021 0.745021
0.350000 10.000000 10.000000 0.540015 0.540015
0.400000 10.000000 10.000000 0.595892 0.595892
0.450000 10.000000 10.000000 0.484320 0.484320
0.500000 10.000000 10.000000 0.521010 0.521010
0.550000 10.000000 10.000000 0.603059 0.603059
regtest/basic/rt63c/ff.reference 0 → 100644
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regtest/basic/rt63c/helix.input.gro 0 → 100644
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regtest/basic/rt63c/helix.pdb 0 → 100644
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ATOM 1 HH31 ACE 1 -9.105 -2.402 21.804 0.00 0.00
ATOM 2 CH3 ACE 1 -8.930 -3.352 22.308 0.00 0.00
ATOM 3 HH32 ACE 1 -9.504 -3.501 23.223 0.00 0.00
ATOM 4 HH33 ACE 1 -9.067 -4.173 21.604 0.00 0.00
ATOM 5 C ACE 1 -7.450 -3.303 22.659 0.00 0.00
ATOM 6 O ACE 1 -6.909 -2.213 22.834 0.00 0.00
ATOM 7 N ALA 2 -6.812 -4.475 22.683 0.00 0.00
ATOM 8 H ALA 2 -7.324 -5.304 22.418 0.00 0.00
ATOM 9 CA ALA 2 -5.397 -4.597 22.969 1.00 1.00
ATOM 10 HA ALA 2 -4.882 -3.860 22.353 0.00 0.00
ATOM 11 CB ALA 2 -5.075 -4.366 24.443 0.00 0.00
ATOM 12 HB1 ALA 2 -4.010 -4.351 24.674 0.00 0.00
ATOM 13 HB2 ALA 2 -5.438 -5.144 25.114 0.00 0.00
ATOM 14 HB3 ALA 2 -5.561 -3.425 24.701 0.00 0.00
ATOM 15 C ALA 2 -4.909 -5.948 22.466 0.00 0.00
ATOM 16 O ALA 2 -4.728 -6.129 21.264 0.00 0.00
ATOM 17 N ALA 3 -4.848 -6.965 23.328 0.00 0.00
ATOM 18 H ALA 3 -5.121 -6.790 24.285 0.00 0.00
ATOM 19 CA ALA 3 -4.722 -8.399 23.159 1.00 1.00
ATOM 20 HA ALA 3 -3.768 -8.522 22.645 0.00 0.00
ATOM 21 CB ALA 3 -4.609 -9.090 24.515 0.00 0.00
ATOM 22 HB1 ALA 3 -3.760 -8.709 25.082 0.00 0.00
ATOM 23 HB2 ALA 3 -4.510 -10.142 24.246 0.00 0.00
ATOM 24 HB3 ALA 3 -5.489 -9.125 25.158 0.00 0.00
ATOM 25 C ALA 3 -5.753 -9.060 22.256 0.00 0.00
ATOM 26 O ALA 3 -5.359 -9.754 21.321 0.00 0.00
ATOM 27 N ALA 4 -7.036 -8.865 22.568 0.00 0.00
ATOM 28 H ALA 4 -7.040 -8.063 23.182 0.00 0.00
ATOM 29 CA ALA 4 -8.201 -9.234 21.789 1.00 1.00
ATOM 30 HA ALA 4 -7.869 -9.845 20.949 0.00 0.00
ATOM 31 CB ALA 4 -9.165 -9.957 22.726 0.00 0.00
ATOM 32 HB1 ALA 4 -8.633 -10.787 23.190 0.00 0.00
ATOM 33 HB2 ALA 4 -10.099 -10.329 22.305 0.00 0.00
ATOM 34 HB3 ALA 4 -9.400 -9.257 23.527 0.00 0.00
ATOM 35 C ALA 4 -8.724 -7.907 21.258 0.00 0.00
ATOM 36 O ALA 4 -8.269 -6.846 21.676 0.00 0.00
ATOM 37 N ALA 5 -9.566 -7.899 20.221 0.00 0.00
ATOM 38 H ALA 5 -9.630 -8.819 19.810 0.00 0.00
ATOM 39 CA ALA 5 -9.923 -6.793 19.356 1.00 1.00
ATOM 40 HA ALA 5 -10.138 -5.948 20.009 0.00 0.00
ATOM 41 CB ALA 5 -8.791 -6.404 18.409 0.00 0.00
ATOM 42 HB1 ALA 5 -8.531 -7.143 17.651 0.00 0.00
ATOM 43 HB2 ALA 5 -7.859 -6.290 18.963 0.00 0.00
ATOM 44 HB3 ALA 5 -8.983 -5.483 17.859 0.00 0.00
ATOM 45 C ALA 5 -11.178 -7.047 18.532 0.00 0.00
ATOM 46 O ALA 5 -11.516 -8.217 18.366 0.00 0.00
ATOM 47 N ALA 6 -11.927 -6.054 18.049 0.00 0.00
ATOM 48 H ALA 6 -11.603 -5.097 18.052 0.00 0.00
ATOM 49 CA ALA 6 -13.240 -6.259 17.469 1.00 1.00
ATOM 50 HA ALA 6 -13.121 -7.160 16.866 0.00 0.00
ATOM 51 CB ALA 6 -14.367 -6.396 18.489 0.00 0.00
ATOM 52 HB1 ALA 6 -15.329 -6.504 17.990 0.00 0.00
ATOM 53 HB2 ALA 6 -14.356 -5.552 19.178 0.00 0.00
ATOM 54 HB3 ALA 6 -14.135 -7.227 19.155 0.00 0.00
ATOM 55 C ALA 6 -13.632 -5.087 16.582 0.00 0.00
ATOM 56 O ALA 6 -13.364 -3.936 16.918 0.00 0.00
ATOM 57 N ALA 7 -14.207 -5.433 15.428 0.00 0.00
ATOM 58 H ALA 7 -14.289 -6.440 15.399 0.00 0.00
ATOM 59 CA ALA 7 -14.898 -4.580 14.482 1.00 1.00
ATOM 60 HA ALA 7 -15.364 -3.792 15.074 0.00 0.00
ATOM 61 CB ALA 7 -13.891 -3.800 13.642 0.00 0.00
ATOM 62 HB1 ALA 7 -14.478 -3.098 13.049 0.00 0.00
ATOM 63 HB2 ALA 7 -13.232 -4.434 13.048 0.00 0.00
ATOM 64 HB3 ALA 7 -13.289 -3.155 14.282 0.00 0.00
ATOM 65 C ALA 7 -15.946 -5.170 13.549 0.00 0.00
ATOM 66 O ALA 7 -17.154 -5.054 13.744 0.00 0.00
ATOM 67 N ALA 8 -15.477 -6.023 12.635 0.00 0.00
ATOM 68 H ALA 8 -14.472 -6.108 12.571 0.00 0.00
ATOM 69 CA ALA 8 -16.137 -7.083 11.902 1.00 1.00
ATOM 70 HA ALA 8 -17.209 -7.030 12.095 0.00 0.00
ATOM 71 CB ALA 8 -15.913 -6.901 10.403 0.00 0.00
ATOM 72 HB1 ALA 8 -16.476 -6.072 9.975 0.00 0.00
ATOM 73 HB2 ALA 8 -16.105 -7.811 9.835 0.00 0.00
ATOM 74 HB3 ALA 8 -14.837 -6.728 10.420 0.00 0.00
ATOM 75 C ALA 8 -15.549 -8.405 12.374 0.00 0.00
ATOM 76 O ALA 8 -14.368 -8.711 12.226 0.00 0.00
ATOM 77 N ALA 9 -16.457 -9.114 13.049 0.00 0.00
ATOM 78 H ALA 9 -17.362 -8.674 13.143 0.00 0.00
ATOM 79 CA ALA 9 -16.134 -10.157 14.001 1.00 1.00
ATOM 80 HA ALA 9 -17.002 -10.541 14.537 0.00 0.00
ATOM 81 CB ALA 9 -15.583 -11.305 13.160 0.00 0.00
ATOM 82 HB1 ALA 9 -14.572 -10.975 12.918 0.00 0.00
ATOM 83 HB2 ALA 9 -16.217 -11.496 12.294 0.00 0.00
ATOM 84 HB3 ALA 9 -15.599 -12.271 13.664 0.00 0.00
ATOM 85 C ALA 9 -15.269 -9.591 15.119 0.00 0.00
ATOM 86 O ALA 9 -15.214 -8.375 15.293 0.00 0.00
ATOM 87 N ALA 10 -14.681 -10.478 15.924 0.00 0.00
ATOM 88 H ALA 10 -14.907 -11.462 15.897 0.00 0.00
ATOM 89 CA ALA 10 -13.672 -10.148 16.910 1.00 1.00
ATOM 90 HA ALA 10 -13.288 -9.136 16.780 0.00 0.00
ATOM 91 CB ALA 10 -14.348 -10.169 18.278 0.00 0.00
ATOM 92 HB1 ALA 10 -14.897 -9.229 18.335 0.00 0.00
ATOM 93 HB2 ALA 10 -13.581 -10.251 19.048 0.00 0.00
ATOM 94 HB3 ALA 10 -14.889 -11.094 18.478 0.00 0.00
ATOM 95 C ALA 10 -12.514 -11.131 16.810 0.00 0.00
ATOM 96 O ALA 10 -12.670 -12.212 16.247 0.00 0.00
ATOM 97 N ALA 11 -11.304 -10.734 17.209 0.00 0.00
ATOM 98 H ALA 11 -11.300 -9.774 17.523 0.00 0.00
ATOM 99 CA ALA 11 -10.028 -11.384 16.987 1.00 1.00
ATOM 100 HA ALA 11 -10.121 -12.468 16.930 0.00 0.00
ATOM 101 CB ALA 11 -9.496 -11.025 15.603 0.00 0.00
ATOM 102 HB1 ALA 11 -8.583 -11.593 15.421 0.00 0.00
ATOM 103 HB2 ALA 11 -9.380 -9.942 15.574 0.00 0.00
ATOM 104 HB3 ALA 11 -10.131 -11.309 14.763 0.00 0.00
ATOM 105 C ALA 11 -9.012 -11.121 18.089 0.00 0.00
ATOM 106 O ALA 11 -9.298 -10.314 18.971 0.00 0.00
ATOM 107 N ALA 12 -7.836 -11.750 18.022 0.00 0.00
ATOM 108 H ALA 12 -7.676 -12.430 17.292 0.00 0.00
ATOM 109 CA ALA 12 -6.626 -11.294 18.676 1.00 1.00
ATOM 110 HA ALA 12 -6.953 -10.965 19.663 0.00 0.00
ATOM 111 CB ALA 12 -5.678 -12.473 18.875 0.00 0.00
ATOM 112 HB1 ALA 12 -5.215 -12.710 17.917 0.00 0.00
ATOM 113 HB2 ALA 12 -6.285 -13.303 19.237 0.00 0.00
ATOM 114 HB3 ALA 12 -4.881 -12.167 19.553 0.00 0.00
ATOM 115 C ALA 12 -6.012 -10.138 17.899 0.00 0.00
ATOM 116 O ALA 12 -6.378 -9.893 16.752 0.00 0.00
ATOM 117 N ALA 13 -5.091 -9.417 18.543 0.00 0.00
ATOM 118 H ALA 13 -5.077 -9.637 19.529 0.00 0.00
ATOM 119 CA ALA 13 -4.233 -8.407 17.956 1.00 1.00
ATOM 120 HA ALA 13 -3.980 -8.732 16.947 0.00 0.00
ATOM 121 CB ALA 13 -4.967 -7.073 17.857 0.00 0.00
ATOM 122 HB1 ALA 13 -4.295 -6.295 17.497 0.00 0.00
ATOM 123 HB2 ALA 13 -5.447 -6.756 18.783 0.00 0.00
ATOM 124 HB3 ALA 13 -5.784 -7.235 17.154 0.00 0.00
ATOM 125 C ALA 13 -2.955 -8.248 18.767 0.00 0.00
ATOM 126 O ALA 13 -1.984 -8.964 18.535 0.00 0.00
ATOM 127 N NME 14 -2.923 -7.389 19.788 0.00 0.00
ATOM 128 H NME 14 -3.729 -6.821 20.007 0.00 0.00
ATOM 129 CH3 NME 14 -1.690 -7.089 20.487 0.00 0.00
ATOM 130 HH31 NME 14 -1.873 -6.629 21.459 0.00 0.00
ATOM 131 HH32 NME 14 -1.152 -6.284 19.986 0.00 0.00
ATOM 132 HH33 NME 14 -1.135 -8.020 20.602 0.00 0.00
END
regtest/basic/rt63c/plumed.dat 0 → 100644
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MOLINFO STRUCTURE=helix.pdb
# length of first lattice vector
cell: CELL
aaaa: MATHEVAL ARG=cell.ax,cell.ay,cell.az FUNC=0.001*(x*x+y*y+z*z) PERIODIC=NO
# rmsd with align!=displace
rmsd: RMSD REFERENCE=align.pdb TYPE=OPTIMAL
FIT_TO_TEMPLATE REFERENCE=align.pdb TYPE=OPTIMAL
# length of first lattice vector
cell2: CELL
aaaa2: MATHEVAL ARG=cell.ax,cell.ay,cell.az FUNC=0.001*(x*x+y*y+z*z) PERIODIC=NO
# rmsd with align!=displace
p8: POSITION ATOM=8
rmsd2: MATHEVAL ARG=p8.x,p8.y,p8.z FUNC=sqrt((x-0.2)^2+(y-0.3)^2+(z-0.4)^2) PERIODIC=NO
PRINT ARG=aaaa,aaaa2,rmsd,rmsd2 FILE=ddd
# here either rmsd or rmsd2 should give the same result:
RESTRAINT ARG=rmsd2 AT=0 SLOPE=1
# here either aaaa or aaaa2 should give the same result:
RESTRAINT ARG=aaaa2 AT=0 SLOPE=1
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