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Commit 563699b9 authored by Marco's avatar Marco
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I thought that maybe not explicitly giving an output format in 

the regtext might produce different results on other architectures so I added
a numeric format keyword to the plumed.dat file of both regtexts.
Also the test .pdb configurations are improved, being now taken from a trajectory rather than
a starting configuration.
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regtest/basic/rt-dimer-0/colvar.reference
+ 1
− 3
View file @ 563699b9
#! FIELDS time dim #! FIELDS time dim
0.000000 3357.740395 0.000000 65.3544
1.000000 3349.712277
2.000000 3353.579829
regtest/basic/rt-dimer-0/deriv.reference
+ 141
− 153
View file @ 563699b9
#! FIELDS time parameter dim #! FIELDS time parameter dim
0.000000 0 -550.7282181126 0.000000 0 -513.1451
0.000000 1 -1112.7237128311 0.000000 1 233.2639
0.000000 2 117.8452179560 0.000000 2 606.2015
0.000000 3 -933.9598265622 0.000000 3 1100.6169
0.000000 4 -795.3734231186 0.000000 4 262.1088
0.000000 5 224.7263314866 0.000000 5 -26.1909
0.000000 6 -1220.1012073335 0.000000 6 932.1110
0.000000 7 -219.5959714758 0.000000 7 -121.6738
0.000000 8 -136.1270427740 0.000000 8 -121.5192
0.000000 9 -1134.3084658863 0.000000 9 -105.1715
0.000000 10 -511.7601412772 0.000000 10 -630.2279
0.000000 11 82.7566038260 0.000000 11 209.9424
0.000000 12 -731.5141477463 0.000000 12 719.1110
0.000000 13 -578.5974025971 0.000000 13 -37.8252
0.000000 14 827.9468292132 0.000000 14 -681.1415
0.000000 15 -850.7535297329 0.000000 15 -1116.5131
0.000000 16 -775.9825371461 0.000000 16 -159.5164
0.000000 17 479.0238824331 0.000000 17 -26.5692
0.000000 18 -1035.3670210906 0.000000 18 442.2021
0.000000 19 429.0216447282 0.000000 19 -331.7043
0.000000 20 547.0980112218 0.000000 20 165.9576
0.000000 21 550.7282181126 0.000000 21 -598.2404
0.000000 22 1112.7237128311 0.000000 22 108.6955
0.000000 23 -117.8452179560 0.000000 23 -54.3478
0.000000 24 933.9598265622 0.000000 24 -66.5490
0.000000 25 795.3734231186 0.000000 25 -1098.6941
0.000000 26 -224.7263314866 0.000000 26 -482.7345
0.000000 27 1220.1012073335 0.000000 27 1182.5617
0.000000 28 219.5959714758 0.000000 28 316.1419
0.000000 29 136.1270427740 0.000000 29 46.8540
0.000000 30 1134.3084658863 0.000000 30 -679.1149
0.000000 31 511.7601412772 0.000000 31 0.0000
0.000000 32 -82.7566038260 0.000000 32 52.2089
0.000000 33 731.5141477463 0.000000 33 700.1068
0.000000 34 578.5974025971 0.000000 34 -50.1711
0.000000 35 -827.9468292132 0.000000 35 -249.9019
0.000000 36 850.7535297329 0.000000 36 -627.4643
0.000000 37 775.9825371461 0.000000 37 -209.0218
0.000000 38 -479.0238824331 0.000000 38 -156.7664
0.000000 39 1035.3670210906 0.000000 39 1206.1609
0.000000 40 -429.0216447282 0.000000 40 47.0274
0.000000 41 -547.0980112218 0.000000 41 -15.6559
0.000000 42 -2047.6601956509 0.000000 42 -899.6905
0.000000 43 -951.3759437313 0.000000 43 -449.8452
0.000000 44 511.6677685462 0.000000 44 613.4962
0.000000 45 -951.3759437313 0.000000 45 -588.6830
0.000000 46 -950.9575138012 0.000000 46 -972.7087
0.000000 47 304.4296725762 0.000000 47 25.5822
0.000000 48 511.6677685463 0.000000 48 -720.1569
0.000000 49 304.4296725764 0.000000 49 -47.9738
0.000000 50 -376.4887823676 0.000000 50 -336.0000
1.000000 0 -550.4393096770 0.000000 51 890.1987
1.000000 1 -1113.5487747510 0.000000 52 850.2120
1.000000 2 111.2156095900 0.000000 53 -9.9967
1.000000 3 -930.6127082645 0.000000 54 -523.1799
1.000000 4 -802.3639589060 0.000000 55 861.7909
1.000000 5 213.4825738259 0.000000 56 400.1340
1.000000 6 -1220.8256104317 0.000000 57 -356.7689
1.000000 7 -215.1706063703 0.000000 58 0.0000
1.000000 8 -136.6936876703 0.000000 59 118.8474
1.000000 9 -1136.0514421492 0.000000 60 991.2517
1.000000 10 -508.0228786885 0.000000 61 -146.9092
1.000000 11 81.8701945417 0.000000 62 110.2169
1.000000 12 -730.9004926469 0.000000 63 123.5038
1.000000 13 -576.7553395198 0.000000 64 123.2685
1.000000 14 829.7722004676 0.000000 65 -61.6343
1.000000 15 -846.2610701626 0.000000 66 513.1451
1.000000 16 -779.6352814440 0.000000 67 -233.2639
1.000000 17 481.0457025987 0.000000 68 -606.2015
1.000000 18 -1025.6008355926 0.000000 69 -1100.6169
1.000000 19 441.0736196895 0.000000 70 -262.1088
1.000000 20 555.8371500815 0.000000 71 26.1909
1.000000 21 550.4393096770 0.000000 72 -932.1110
1.000000 22 1113.5487747510 0.000000 73 121.6738
1.000000 23 -111.2156095900 0.000000 74 121.5192
1.000000 24 930.6127082645 0.000000 75 105.1715
1.000000 25 802.3639589060 0.000000 76 630.2279
1.000000 26 -213.4825738259 0.000000 77 -209.9424
1.000000 27 1220.8256104317 0.000000 78 -719.1110
1.000000 28 215.1706063703 0.000000 79 37.8252
1.000000 29 136.6936876703 0.000000 80 681.1415
1.000000 30 1136.0514421492 0.000000 81 1116.5131
1.000000 31 508.0228786885 0.000000 82 159.5164
1.000000 32 -81.8701945417 0.000000 83 26.5692
1.000000 33 730.9004926469 0.000000 84 -442.2021
1.000000 34 576.7553395198 0.000000 85 331.7043
1.000000 35 -829.7722004676 0.000000 86 -165.9576
1.000000 36 846.2610701626 0.000000 87 598.2404
1.000000 37 779.6352814440 0.000000 88 -108.6955
1.000000 38 -481.0457025987 0.000000 89 54.3478
1.000000 39 1025.6008355926 0.000000 90 66.5490
1.000000 40 -441.0736196895 0.000000 91 1098.6941
1.000000 41 -555.8371500815 0.000000 92 482.7345
1.000000 42 -2030.4957204730 0.000000 93 -1182.5617
1.000000 43 -951.5853913325 0.000000 94 -316.1419
1.000000 44 506.7839235380 0.000000 95 -46.8540
1.000000 45 -951.5853913326 0.000000 96 679.1149
1.000000 46 -959.4078999864 0.000000 97 0.0000
1.000000 47 300.6550075680 0.000000 98 -52.2089
1.000000 48 506.7839235381 0.000000 99 -700.1068
1.000000 49 300.6550075681 0.000000 100 50.1711
1.000000 50 -377.1744005113 0.000000 101 249.9019
2.000000 0 -550.6778249834 0.000000 102 627.4643
2.000000 1 -1113.0928894820 0.000000 103 209.0218
2.000000 2 114.5482226356 0.000000 104 156.7664
2.000000 3 -932.2507327832 0.000000 105 -1206.1609
2.000000 4 -798.8798544361 0.000000 106 -47.0274
2.000000 5 219.3212511934 0.000000 107 15.6559
2.000000 6 -1220.4952472059 0.000000 108 899.6905
2.000000 7 -217.1270099739 0.000000 109 449.8452
2.000000 8 -136.5523398262 0.000000 110 -613.4962
2.000000 9 -1135.1512302280 0.000000 111 588.6830
2.000000 10 -509.9370896593 0.000000 112 972.7087
2.000000 11 82.4540312574 0.000000 113 -25.5822
2.000000 12 -731.3872094752 0.000000 114 720.1569
2.000000 13 -577.6817894215 0.000000 115 47.9738
2.000000 14 828.6980782496 0.000000 116 336.0000
2.000000 15 -848.5162672004 0.000000 117 -890.1987
2.000000 16 -777.8059000515 0.000000 118 -850.2120
2.000000 17 480.0336127023 0.000000 119 9.9967
2.000000 18 -1030.3960149949 0.000000 120 523.1799
2.000000 19 434.8098746145 0.000000 121 -861.7909
2.000000 20 551.8910628978 0.000000 122 -400.1340
2.000000 21 550.6778249834 0.000000 123 356.7689
2.000000 22 1113.0928894820 0.000000 124 0.0000
2.000000 23 -114.5482226356 0.000000 125 -118.8474
2.000000 24 932.2507327832 0.000000 126 -991.2517
2.000000 25 798.8798544361 0.000000 127 146.9092
2.000000 26 -219.3212511934 0.000000 128 -110.2169
2.000000 27 1220.4952472059 0.000000 129 -123.5038
2.000000 28 217.1270099739 0.000000 130 -123.2685
2.000000 29 136.5523398262 0.000000 131 61.6343
2.000000 30 1135.1512302280 0.000000 132 -56.4135
2.000000 31 509.9370896593 0.000000 133 -15.0971
2.000000 32 -82.4540312574 0.000000 134 4.5817
2.000000 33 731.3872094752 0.000000 135 -15.0971
2.000000 34 577.6817894215 0.000000 136 -24.1142
2.000000 35 -828.6980782496 0.000000 137 -2.9964
2.000000 36 848.5162672004 0.000000 138 4.5817
2.000000 37 777.8059000515 0.000000 139 -2.9964
2.000000 38 -480.0336127023 0.000000 140 -6.4546
2.000000 39 1030.3960149949
2.000000 40 -434.8098746145
2.000000 41 -551.8910628978
2.000000 42 -2039.0111752402
2.000000 43 -951.4381808243
2.000000 44 509.4080074689
2.000000 45 -951.4381808241
2.000000 46 -955.0210968550
2.000000 47 302.6150172129
2.000000 48 509.4080074691
2.000000 49 302.6150172131
2.000000 50 -376.9134753879
regtest/basic/rt-dimer-0/plumed.dat
+ 2
− 2
View file @ 563699b9
dim: DIMER ALLATOMS Q=0.5 TEMP=300 DSIGMA=0.002 dim: DIMER ALLATOMS Q=0.5 TEMP=300 DSIGMA=0.002
DUMPDERIVATIVES ARG=dim STRIDE=1 FILE=deriv DUMPDERIVATIVES ARG=dim STRIDE=1 FILE=deriv FMT=%8.4f
PRINT ARG=dim FILE=colvar PRINT ARG=dim FILE=colvar FMT=%8.4f
regtest/basic/rt-dimer-1/colvar.reference
+ 3
− 1
View file @ 563699b9
#! FIELDS time dim #! FIELDS time dim
0.000000 0.049767 0.000000 17.0721
1.000000 16.8868
2.000000 12.1518
regtest/basic/rt-dimer-1/deriv.reference
+ 99
− 33
View file @ 563699b9
#! FIELDS time parameter dim #! FIELDS time parameter dim
0.000000 0 -124.1476679724 0.000000 0 -26.3036
0.000000 1 0.0000000000 0.000000 1 1130.5798
0.000000 2 0.0000000000 0.000000 2 0.0000
0.000000 3 -124.0890796024 0.000000 3 -251.5210
0.000000 4 0.0000000000 0.000000 4 -1183.6796
0.000000 5 0.0000000000 0.000000 5 -59.1797
0.000000 6 -124.0890796024 0.000000 6 835.3847
0.000000 7 0.0000000000 0.000000 7 696.1406
0.000000 8 0.0000000000 0.000000 8 250.6048
0.000000 9 -124.0890796024 0.000000 9 -154.4567
0.000000 10 0.0000000000 0.000000 10 803.1574
0.000000 11 0.0000000000 0.000000 11 -710.5069
0.000000 12 124.1476679724 0.000000 12 26.3036
0.000000 13 0.0000000000 0.000000 13 -1130.5798
0.000000 14 0.0000000000 0.000000 14 0.0000
0.000000 15 124.0890796024 0.000000 15 251.5210
0.000000 16 0.0000000000 0.000000 16 1183.6796
0.000000 17 0.0000000000 0.000000 17 59.1797
0.000000 18 124.0890796024 0.000000 18 -835.3847
0.000000 19 0.0000000000 0.000000 19 -696.1406
0.000000 20 0.0000000000 0.000000 20 -250.6048
0.000000 21 124.0890796024 0.000000 21 154.4567
0.000000 22 0.0000000000 0.000000 22 -803.1574
0.000000 23 0.0000000000 0.000000 23 710.5069
0.000000 24 -0.0992876250 0.000000 24 -3.0136
0.000000 25 0.0000000000 0.000000 25 -3.5859
0.000000 26 0.0000000000 0.000000 26 -1.2077
0.000000 27 -0.0000000000 0.000000 27 -3.5859
0.000000 28 0.0000000000 0.000000 28 -18.1594
0.000000 29 0.0000000000 0.000000 29 0.7474
0.000000 30 0.0000000000 0.000000 30 -1.2077
0.000000 31 0.0000000000 0.000000 31 0.7474
0.000000 32 0.0000000000 0.000000 32 -1.8834
1.000000 0 807.2418
1.000000 1 873.1503
1.000000 2 181.2131
1.000000 3 43.4572
1.000000 4 804.0298
1.000000 5 847.4663
1.000000 6 905.4682
1.000000 7 658.5271
1.000000 8 -27.4495
1.000000 9 -203.0650
1.000000 10 -304.6056
1.000000 11 981.4513
1.000000 12 -807.2418
1.000000 13 -873.1503
1.000000 14 -181.2131
1.000000 15 -43.4572
1.000000 16 -804.0298
1.000000 17 -847.4663
1.000000 18 -905.4682
1.000000 19 -658.5271
1.000000 20 27.4495
1.000000 21 203.0650
1.000000 22 304.6056
1.000000 23 -981.4513
1.000000 24 -7.0740
1.000000 25 -6.7951
1.000000 26 -0.3780
1.000000 27 -6.7951
1.000000 28 -9.4573
1.000000 29 -3.1469
1.000000 30 -0.3780
1.000000 31 -3.1469
1.000000 32 -6.3533
2.000000 0 1047.3196
2.000000 1 -541.1138
2.000000 2 209.4639
2.000000 3 73.7877
2.000000 4 -369.0088
2.000000 5 -1082.4619
2.000000 6 -382.4724
2.000000 7 -327.8372
2.000000 8 -327.8632
2.000000 9 422.5760
2.000000 10 -883.5464
2.000000 11 76.8620
2.000000 12 -1047.3196
2.000000 13 541.1138
2.000000 14 -209.4639
2.000000 15 -73.7877
2.000000 16 369.0088
2.000000 17 1082.4619
2.000000 18 382.4724
2.000000 19 327.8372
2.000000 20 327.8632
2.000000 21 -422.5760
2.000000 22 883.5464
2.000000 23 -76.8620
2.000000 24 -7.0387
2.000000 25 4.0998
2.000000 26 -1.2462
2.000000 27 4.0998
2.000000 28 -4.4598
2.000000 29 -0.9942
2.000000 30 -1.2462
2.000000 31 -0.9942
2.000000 32 -5.2263
regtest/basic/rt-dimer-1/plumed.dat
+ 2
− 2
View file @ 563699b9
dim: DIMER NATOMS=22 ATOMS=1,3,14,17 Q=0.5 TEMP=300 DSIGMA=0.002 dim: DIMER NATOMS=22 ATOMS=1,3,14,17 Q=0.5 TEMP=300 DSIGMA=0.002
DUMPDERIVATIVES ARG=dim STRIDE=1 FILE=deriv DUMPDERIVATIVES ARG=dim STRIDE=1 FILE=deriv FMT=%8.4f
PRINT ARG=dim FILE=colvar PRINT ARG=dim FILE=colvar FMT=%8.4f
regtest/trajectories/dimer/aladip.pdb
+ 0
− 2
View file @ 563699b9
...@@ -25,7 +25,6 @@ ATOM 19 CH3 NME X 3 50.616 53.639 50.256 1.00 0.00 C ...@@ -25,7 +25,6 @@ ATOM 19 CH3 NME X 3 50.616 53.639 50.256 1.00 0.00 C
ATOM 20 1HH3 NME X 3 51.006 53.839 51.221 1.00 0.00 H ATOM 20 1HH3 NME X 3 51.006 53.839 51.221 1.00 0.00 H
ATOM 21 2HH3 NME X 3 51.106 54.293 49.435 1.00 0.00 H ATOM 21 2HH3 NME X 3 51.106 54.293 49.435 1.00 0.00 H
ATOM 22 3HH3 NME X 3 49.630 53.896 50.305 1.00 0.00 H ATOM 22 3HH3 NME X 3 49.630 53.896 50.305 1.00 0.00 H
END
ATOM 23 CH3 ACE X 1 47.063 47.854 49.997 1.00 0.00 C ATOM 23 CH3 ACE X 1 47.063 47.854 49.997 1.00 0.00 C
ATOM 24 1HH3 ACE X 1 46.770 46.927 50.624 1.00 0.00 H ATOM 24 1HH3 ACE X 1 46.770 46.927 50.624 1.00 0.00 H
ATOM 25 2HH3 ACE X 1 46.351 48.721 50.271 1.00 0.00 H ATOM 25 2HH3 ACE X 1 46.351 48.721 50.271 1.00 0.00 H
...@@ -48,7 +47,6 @@ ATOM 41 CH3 NME X 3 50.633 53.611 50.243 1.00 0.00 C ...@@ -48,7 +47,6 @@ ATOM 41 CH3 NME X 3 50.633 53.611 50.243 1.00 0.00 C
ATOM 42 1HH3 NME X 3 51.012 53.839 51.219 1.00 0.00 H ATOM 42 1HH3 NME X 3 51.012 53.839 51.219 1.00 0.00 H
ATOM 43 2HH3 NME X 3 51.079 54.297 49.432 1.00 0.00 H ATOM 43 2HH3 NME X 3 51.079 54.297 49.432 1.00 0.00 H
ATOM 44 3HH3 NME X 3 49.628 53.894 50.306 1.00 0.00 H ATOM 44 3HH3 NME X 3 49.628 53.894 50.306 1.00 0.00 H
END
ATOM 45 CH3 ACE X 1 47.057 47.857 50.003 1.00 0.00 C ATOM 45 CH3 ACE X 1 47.057 47.857 50.003 1.00 0.00 C
ATOM 46 1HH3 ACE X 1 46.791 46.932 50.624 1.00 0.00 H ATOM 46 1HH3 ACE X 1 46.791 46.932 50.624 1.00 0.00 H
ATOM 47 2HH3 ACE X 1 46.363 48.720 50.269 1.00 0.00 H ATOM 47 2HH3 ACE X 1 46.363 48.720 50.269 1.00 0.00 H
......
regtest/trajectories/dimer/aladip_wsol.pdb
+ 4647
− 1555
View file @ 563699b9
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