Action: READ

Module generic
Description Usage
Read quantities from a colvar file. used in 5 tutorialsused in 17 eggs

Further details and examples

Read quantities from a colvar file.

This Action can be used with driver to read in a colvar file that was generated during an MD simulation. The following example shows how this works.

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS INPUTFILES=regtest/basic/rt-fametad-1/Input-COLVAR
sum_abs: READRead quantities from a colvar file. This action has hidden defaults. More details VALUESthe values to read from the file=sum_abs FILEthe name of the file from which to read these quantities=
regtest/basic/rt-fametad-1/Input-COLVAR
Click here to see an extract from this file.
×

FILE: regtest/basic/rt-fametad-1/Input-COLVAR

#! FIELDS time sum_abs
 0.000000    2.573995685777813e-01
 1.000000    2.808644607440173e-01
 2.000000    2.388030517838102e-01
 3.000000    2.338311778988506e-01
 4.000000    2.545516057443710e-01
 5.000000    1.896528759501126e-01
 6.000000    2.082371498064038e-01
 7.000000    1.820266531965062e-01
 8.000000    4.050893524907833e-01
 9.000000    3.358144209806148e-01
 10.000000    2.709454044703344e-01
 11.000001    2.547265360892176e-01
 12.000001    3.064370620517174e-01
 13.000001    3.505324740992907e-01
 14.000001    2.190999560317414e-01
 15.000001    3.189065207635467e-01
 16.000001    3.000609444813501e-01
 17.000001    2.057066176408750e-01
 18.000001    2.908132526841631e-01
 19.000001    1.904904651547845e-01
 20.000001    2.407095373683305e-01
 21.000001    3.216311528325366e-01
 22.000001    3.491829378061025e-01
 23.000001    3.783253800497334e-01
 24.000001    3.402744774908654e-01
 25.000001    3.679815803838902e-01
 26.000001    2.607246875973884e-01
 27.000001    3.595832174696479e-01
 28.000001    3.222692810117627e-01
 29.000001    3.003695147127406e-01
 30.000001    1.662427904284903e-01
 31.000001    3.594182591961172e-01
 32.000002    2.628521943800115e-01
 33.000002    2.466498150091782e-01
 34.000002    2.907455210908650e-01
 35.000002    2.371405100588842e-01
 36.000002    1.750641098388233e-01
 37.000002    3.790127629959251e-01
 38.000002    4.147042687835962e-01
 39.000002    3.597157182573542e-01
 40.000002    3.389039820374391e-01
 41.000002    2.255031943297208e-01
 42.000002    3.091436504217430e-01
 43.000002    1.743568007445536e-01
 44.000002    2.334647325862707e-01
 45.000002    2.257675818347779e-01
 46.000002    3.996871328612751e-01
 47.000002    3.094116726040716e-01
 48.000002    2.027235056680874e-01
 49.000002    2.673414857597688e-01
 50.000002    2.916794259496168e-01
 51.000002    3.292025590925996e-01
 52.000002    2.373538954257433e-01
 53.000003    3.926209050491571e-01
 54.000003    2.901598529824529e-01
 55.000003    2.306531124608514e-01
 56.000003    3.470363201171859e-01
 57.000003    2.841238526351582e-01
 58.000003    3.604364905963292e-01
 59.000003    3.259728377174720e-01
 60.000003    3.289565699332488e-01
 61.000003    3.924067183515320e-01
 62.000003    2.690788598133806e-01
 63.000003    4.354984517084572e-01
 64.000003    2.436277408312573e-01
 65.000003    3.703780649852265e-01
 66.000003    4.328821727307227e-01
 67.000003    4.173530892042359e-01
 68.000003    3.971866787119422e-01
 69.000003    3.476482922980171e-01
 70.000003    1.935187141800251e-01
 71.000003    1.959277335251484e-01
 72.000003    4.293145326452090e-01
 73.000003    4.145504303302811e-01
 74.000004    2.583763595775005e-01
 75.000004    2.848538930968699e-01
 76.000004    3.689178187401129e-01
 77.000004    2.861547652622837e-01
 78.000004    2.194203272976653e-01
 79.000004    2.150751768650956e-01
 80.000004    4.417803234071846e-01
 81.000004    3.014124061167107e-01
 82.000004    2.445568367776431e-01
 83.000004    3.705610293990234e-01
 84.000004    3.371304665097392e-01
 85.000004    3.199345282222015e-01
 86.000004    4.048426241504061e-01
 87.000004    2.338393619036179e-01
 88.000004    2.618526880105485e-01
 89.000004    1.999528462243149e-01
 90.000004    2.803427148653018e-01
 91.000004    2.696373105364500e-01
 92.000004    3.714088541330838e-01
 93.000004    2.617878904143192e-01
 94.000004    3.401159206181693e-01
 95.000005    2.654193705157792e-01
 96.000005    3.102662267122588e-01
 97.000005    4.417967122523199e-01
 98.000005    2.343482107852504e-01
 99.000005    1.926777731982127e-01
 100.000005    2.520121745917367e-01
 101.000005    3.185490162733534e-01
 102.000005    3.972905447379251e-01
 103.000005    2.441165051640122e-01
 104.000005    2.221906711171487e-01
 105.000005    2.521966269821222e-01
 106.000005    1.764422076500425e-01
 107.000005    3.964604140565903e-01
 108.000005    4.359253484610757e-01
 109.000005    2.428794727666250e-01
 110.000005    2.484101909601867e-01
 111.000005    2.550419442870552e-01
 112.000005    2.068895127710110e-01
 113.000005    3.908650387584589e-01
 114.000005    2.584566267613805e-01
 115.000005    2.508051850177675e-01
 116.000006    2.841577624675563e-01
 117.000006    3.147428297713805e-01
 118.000006    3.442451444771333e-01
 119.000006    3.583642213302888e-01
 120.000006    2.158242252678579e-01
 121.000006    3.010343677979283e-01
 122.000006    2.437380992840285e-01
 123.000006    2.302195136903848e-01
 124.000006    2.568081601869469e-01
 125.000006    1.950778901003879e-01
 126.000006    2.135360933857036e-01
 127.000006    3.647861248901131e-01
 128.000006    3.390540590620605e-01
 129.000006    3.883961270381328e-01
 130.000006    3.181896942808664e-01
 131.000006    2.492134489311857e-01
 132.000006    4.197406053957075e-01
 133.000006    3.345249799447446e-01
 134.000006    2.162342775437300e-01
 135.000006    3.044858144479707e-01
 136.000006    3.187659323808723e-01
 137.000007    3.917533324286606e-01
 138.000007    1.819188860705302e-01
 139.000007    2.442136197699639e-01
 140.000007    2.410804873534188e-01
 141.000007    3.705056670410870e-01
 142.000007    2.596755604507863e-01
 143.000007    2.576893154688571e-01
 144.000007    3.335550183791997e-01
 145.000007    2.197317269721956e-01
 146.000007    2.580244531444330e-01
 147.000007    5.074025613686975e-01
 148.000007    6.922569570610256e-01
 149.000007    8.350020236233408e-01
 150.000007    7.643288864353646e-01
 151.000007    7.331279624626694e-01
 152.000007    8.577594423585888e-01
 153.000007    7.125367723747373e-01
 154.000007    7.363731023240252e-01
 155.000007    7.467899644347973e-01
 156.000007    7.931257978180847e-01
 157.000007    7.778706119742582e-01
 158.000008    7.694504774591154e-01
 159.000008    7.855901936070381e-01
 160.000008    7.565061523201652e-01
 161.000008    7.783552795312988e-01
 162.000008    8.210201687109571e-01
 163.000008    8.943249445432165e-01
 164.000008    7.239485084278602e-01
 165.000008    8.881937558974977e-01
 166.000008    7.857607801766643e-01
 167.000008    7.823481558614901e-01
 168.000008    8.085993907484226e-01
 169.000008    7.049856619973440e-01
 170.000008    7.794736794461753e-01
 171.000008    7.398500375919714e-01
 172.000008    8.195140566804866e-01
 173.000008    8.854748040070306e-01
 174.000008    8.401741889427012e-01
 175.000008    9.549300500378984e-01
 176.000008    9.241817814338401e-01
 177.000008    8.553709668212137e-01
 178.000008    9.375559405842896e-01
 179.000009    8.526745953444749e-01
 180.000009    9.740290949207988e-01
 181.000009    8.871429781854550e-01
 182.000009    7.897518110350888e-01
 183.000009    8.642314120684643e-01
 184.000009    9.520469324361746e-01
 185.000009    8.644627670374140e-01
 186.000009    8.439913878501130e-01
 187.000009    9.243560503916659e-01
 188.000009    9.025894789901834e-01
 189.000009    7.588940263118590e-01
 190.000009    7.263835749733036e-01
 191.000009    8.332115721196766e-01
 192.000009    8.211657100847689e-01
 193.000009    8.449870658194392e-01
 194.000009    8.908670900266055e-01
 195.000009    8.804527996221376e-01
 196.000009    8.330554556858161e-01
 197.000009    7.783640302358340e-01
 198.000009    8.664452284485922e-01
 199.000009    8.612768857973366e-01
 200.000009    7.027086507788267e-01
IGNORE_FORCES use this flag if the forces added by any bias can be safely ignored
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=sum_abs STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=colvar

The input file Input-COLVAR is a colvar file that was generated using a PRINT command. The instruction VALUES=sum_abs tells PLUMED that we want to read the column headed sum_abs from that file. The value outputted from a read command is thus always a scalar.

The IGNORE_FORCES flag tells PLUMED that any forces that are applied on this action can be safely ignored. If you try to run a simulation in which a bias acts upon a quantity that is read in from a file using a READ command PLUMED will crash with an error.

Dealing with components

The following example provides another example where the READ command is used:

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS INPUTFILES=regtest/basic/rt41/input_colvar
r1: READRead quantities from a colvar file. This action has hidden defaults. More details VALUESthe values to read from the file=p2.X  FILEthe name of the file from which to read these quantities=
regtest/basic/rt41/input_colvar
Click here to see an extract from this file.
×

FILE: regtest/basic/rt41/input_colvar

#! FIELDS time p2.X p2.Y p2.zzz p3.X p3.Y p3.zzz
 0.000000   1.9434   2.9434   0.0001   1.9434   2.9434   0.0001
 0.250000   1.0090   2.0090   0.0001   1.0090   2.0090   0.0001
 0.500000   1.0579   2.0579   0.0001   1.0579   2.0579   0.0001
 0.750000   1.0331   2.0331   0.0000   1.0331   2.0331   0.0000
 1.000000   1.3768   2.3768   0.0001   1.3768   2.3768   0.0001
 1.250000   1.4149   2.4149   0.0000   1.4149   2.4149   0.0000
 1.500000   1.0652   2.0652   0.0001   1.0652   2.0652   0.0001
 1.750000   1.0157   2.0157   0.0000   1.0157   2.0157   0.0000
 2.000000   1.1453   2.1453   0.0001   1.1453   2.1453   0.0001
 2.250000   1.3270   2.3270   0.0000   1.3270   2.3270   0.0000
 2.500000   1.0513   2.0513   0.0000   1.0513   2.0513   0.0000
 2.750000   1.3269   2.3269   0.0000   1.3269   2.3269   0.0000
 3.000000   1.0317   2.0317   0.0001   1.0317   2.0317   0.0001
 3.250000   3.1167   4.1167   0.0001   3.1167   4.1167   0.0001
 3.500000   1.2525   2.2525   0.0001   1.2525   2.2525   0.0001
 3.750000   1.2615   2.2615   0.0001   1.2615   2.2615   0.0001
 4.000000   1.4116   2.4116   0.0001   1.4116   2.4116   0.0001
 4.250000   2.2825   3.2825   0.0001   2.2825   3.2825   0.0001
 4.500000   2.0832   3.0832   0.0000   2.0832   3.0832   0.0000
 4.750000   1.5973   2.5973   0.0001   1.5973   2.5973   0.0001
 5.000000   1.3261   2.3261   0.0001   1.3261   2.3261   0.0001
 5.250000   2.4515   3.4515   0.0001   2.4515   3.4515   0.0001
 5.500000   2.5412   3.5412   0.0001   2.5412   3.5412   0.0001
 5.750000   1.8538   2.8538   0.0000   1.8538   2.8538   0.0000
 6.000000   1.3933   2.3933   0.0001   1.3933   2.3933   0.0001
 6.250000   1.7948   2.7948   0.0000   1.7948   2.7948   0.0000
 6.500000   3.8916   4.8916   0.0001   3.8916   4.8916   0.0001
 6.750000   2.4106   3.4106   0.0001   2.4106   3.4106   0.0001
 7.000000   2.9130   3.9130   0.0000   2.9130   3.9130   0.0000
 7.250000   2.7856   3.7856   0.0000   2.7856   3.7856   0.0000
 7.500000   3.0248   4.0248   0.0001   3.0248   4.0248   0.0001
 7.750000   3.0256   4.0256   0.0001   3.0256   4.0256   0.0001
 8.000000   2.8465   3.8465   0.0001   2.8465   3.8465   0.0001
 8.250000   1.7385   2.7385   0.0001   1.7385   2.7385   0.0001
 8.500000   3.2267   4.2267   0.0001   3.2267   4.2267   0.0001
 8.750000   3.4119   4.4119   0.0000   3.4119   4.4119   0.0000
 9.000000   2.6281   3.6281   0.0000   2.6281   3.6281   0.0000
 9.250000   2.4505   3.4505   0.0001   2.4505   3.4505   0.0001
 9.500000   2.9935   3.9935   0.0001   2.9935   3.9935   0.0001
 9.750000   4.2826   5.2826   0.0001   4.2826   5.2826   0.0001
 10.000000   3.1900   4.1900   0.0001   3.1900   4.1900   0.0001
 10.250000   3.5456   4.5456   0.0000   3.5456   4.5456   0.0000
 10.500000   3.5451   4.5451   0.0000   3.5451   4.5451   0.0000
 10.750000   4.1587   5.1587   0.0001   4.1587   5.1587   0.0001
 11.000000   3.9178   4.9178   0.0000   3.9178   4.9178   0.0000
 11.250000   3.8826   4.8826   0.0001   3.8826   4.8826   0.0001
 11.500000   3.2615   4.2615   0.0001   3.2615   4.2615   0.0001
 11.750000   4.2869   5.2869   0.0001   4.2869   5.2869   0.0001
 12.000000   4.5757   5.5757   0.0000   4.5757   5.5757   0.0000
 12.250000   3.2142   4.2142   0.0000   3.2142   4.2142   0.0000
 12.500000   3.9086   4.9086   0.0001   3.9086   4.9086   0.0001
 12.750000   3.7618   4.7618   0.0001   3.7618   4.7618   0.0001
 13.000000   4.8157   5.8157   0.0001   4.8157   5.8157   0.0001
 13.250000   3.9568   4.9568   0.0001   3.9568   4.9568   0.0001
 13.500000   4.8524   5.8524   0.0000   4.8524   5.8524   0.0000
 13.750000   4.4105   5.4105   0.0000   4.4105   5.4105   0.0000
 14.000000   4.9450   5.9450   0.0001   4.9450   5.9450   0.0001
 14.250000   4.7719   5.7719   0.0001   4.7719   5.7719   0.0001
 14.500000   4.5365   5.5365   0.0001   4.5365   5.5365   0.0001
 14.750000   4.0972   5.0972   0.0001   4.0972   5.0972   0.0001
 15.000000   5.5554   6.5554   0.0001   5.5554   6.5554   0.0001
 15.250000   5.1352   6.1352   0.0001   5.1352   6.1352   0.0001
 15.500000   4.2067   5.2067   0.0000   4.2067   5.2067   0.0000
 15.750000   4.5249   5.5249   0.0001   4.5249   5.5249   0.0001
 16.000000   4.7725   5.7725   0.0001   4.7725   5.7725   0.0001
 16.250000   5.9837   6.9837   0.0001   5.9837   6.9837   0.0001
 16.500000   4.7753   5.7753   0.0000   4.7753   5.7753   0.0000
 16.750000   6.0804   7.0804   0.0001   6.0804   7.0804   0.0001
 17.000000   5.7243   6.7243   0.0000   5.7243   6.7243   0.0000
 17.250000   6.0755   7.0755   0.0001   6.0755   7.0755   0.0001
 17.500000   5.7907   6.7907   0.0000   5.7907   6.7907   0.0000
 17.750000   5.5556   6.5556   0.0001   5.5556   6.5556   0.0001
 18.000000   5.4734   6.4734   0.0001   5.4734   6.4734   0.0001
 18.250000   6.8349   7.8349   0.0001   6.8349   7.8349   0.0001
 18.500000   6.1115   7.1115   0.0001   6.1115   7.1115   0.0001
 18.750000   5.4763   6.4763   0.0001   5.4763   6.4763   0.0001
 19.000000   6.0577   7.0577   0.0000   6.0577   7.0577   0.0000
 19.250000   5.8285   6.8285   0.0001   5.8285   6.8285   0.0001
 19.500000   5.8165   6.8165   0.0001   5.8165   6.8165   0.0001
 19.750000   5.4695   6.4695   0.0000   5.4695   6.4695   0.0000
 20.000000   6.8811   7.8811   0.0000   6.8811   7.8811   0.0000
 20.250000   7.1282   8.1282   0.0000   7.1282   8.1282   0.0000
 20.500000   7.0992   8.0992   0.0001   7.0992   8.0992   0.0001
 20.750000   6.0105   7.0105   0.0001   6.0105   7.0105   0.0001
 21.000000   6.8671   7.8671   0.0000   6.8671   7.8671   0.0000
 21.250000   6.2864   7.2864   0.0001   6.2864   7.2864   0.0001
 21.500000   7.2471   8.2471   0.0000   7.2471   8.2471   0.0000
 21.750000   7.2481   8.2481   0.0000   7.2481   8.2481   0.0000
 22.000000   5.9782   6.9782   0.0001   5.9782   6.9782   0.0001
 22.250000   6.8523   7.8523   0.0001   6.8523   7.8523   0.0001
 22.500000   6.8326   7.8326   0.0001   6.8326   7.8326   0.0001
 22.750000   6.5175   7.5175   0.0000   6.5175   7.5175   0.0000
 23.000000   6.4000   7.4000   0.0000   6.4000   7.4000   0.0000
 23.250000   8.0028   9.0028   0.0000   8.0028   9.0028   0.0000
 23.500000   8.1695   9.1695   0.0000   8.1695   9.1695   0.0000
 23.750000   7.9851   8.9851   0.0001   7.9851   8.9851   0.0001
 24.000000   6.8908   7.8908   0.0001   6.8908   7.8908   0.0001
 24.250000   7.4686   8.4686   0.0001   7.4686   8.4686   0.0001
 24.500000   7.0070   8.0070   0.0001   7.0070   8.0070   0.0001
 24.750000   8.5092   9.5092   0.0001   8.5092   9.5092   0.0001
 25.000000   8.1518   9.1518   0.0000   8.1518   9.1518   0.0000
 25.250000   7.3926   8.3926   0.0001   7.3926   8.3926   0.0001
 25.500000   7.9078   8.9078   0.0001   7.9078   8.9078   0.0001
 25.750000   7.3901   8.3901   0.0001   7.3901   8.3901   0.0001
 26.000000   7.5108   8.5108   0.0000   7.5108   8.5108   0.0000
 26.250000   7.3993   8.3993   0.0000   7.3993   8.3993   0.0000
 26.500000   9.0054  10.0054   0.0000   9.0054  10.0054   0.0000
 26.750000   9.0212  10.0212   0.0001   9.0212  10.0212   0.0001
 27.000000   9.2067  10.2067   0.0000   9.2067  10.2067   0.0000
 27.250000   7.3974   8.3974   0.0001   7.3974   8.3974   0.0001
 27.500000   8.4983   9.4983   0.0000   8.4983   9.4983   0.0000
 27.750000   8.4074   9.4074   0.0001   8.4074   9.4074   0.0001
 28.000000   9.4812  10.4812   0.0000   9.4812  10.4812   0.0000
 28.250000   8.9480   9.9480   0.0000   8.9480   9.9480   0.0000
 28.500000   8.8156   9.8156   0.0001   8.8156   9.8156   0.0001
 28.750000   9.3383  10.3383   0.0001   9.3383  10.3383   0.0001
 29.000000   8.6766   9.6766   0.0001   8.6766   9.6766   0.0001
 29.250000   8.8167   9.8167   0.0001   8.8167   9.8167   0.0001
 29.500000   8.8586   9.8586   0.0000   8.8586   9.8586   0.0000
 29.750000   9.7681  10.7681   0.0000   9.7681  10.7681   0.0000
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 30.250000  10.2048  11.2048   0.0000  10.2048  11.2048   0.0000
 30.500000   8.8600   9.8600   0.0000   8.8600   9.8600   0.0000
 30.750000   9.2746  10.2746   0.0000   9.2746  10.2746   0.0000
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 31.250000  10.3959  11.3959   0.0000  10.3959  11.3959   0.0000
 31.500000  10.0084  11.0084   0.0001  10.0084  11.0084   0.0001
 31.750000   9.8521  10.8521   0.0000   9.8521  10.8521   0.0000
 32.000000  10.3120  11.3120   0.0001  10.3120  11.3120   0.0001
 32.250000   9.5696  10.5696   0.0001   9.5696  10.5696   0.0001
 32.500000  10.2229  11.2229   0.0001  10.2229  11.2229   0.0001
 32.750000   9.2246  10.2246   0.0000   9.2246  10.2246   0.0000
 33.000000  11.0408  12.0408   0.0000  11.0408  12.0408   0.0000
 33.250000  10.9355  11.9355   0.0001  10.9355  11.9355   0.0001
 33.500000  11.0212  12.0212   0.0001  11.0212  12.0212   0.0001
 33.750000   9.9950  10.9950   0.0000   9.9950  10.9950   0.0000
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 37.250000  11.5190  12.5190   0.0000  11.5190  12.5190   0.0000
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 38.500000  12.3989  13.3989   0.0001  12.3989  13.3989   0.0001
 38.750000  11.1104  12.1104   0.0001  11.1104  12.1104   0.0001
 39.000000  11.8881  12.8881   0.0001  11.8881  12.8881   0.0001
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 39.500000  13.5494  14.5494   0.0000  13.5494  14.5494   0.0000
 39.750000  13.2306  14.2306   0.0001  13.2306  14.2306   0.0001
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 41.250000  12.9117  13.9117   0.0001  12.9117  13.9117   0.0001
 41.500000  12.9911  13.9911   0.0000  12.9911  13.9911   0.0000
 41.750000  13.9208  14.9208   0.0001  13.9208  14.9208   0.0001
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 42.500000  12.8370  13.8370   0.0000  12.8370  13.8370   0.0000
 42.750000  14.3876  15.3876   0.0000  14.3876  15.3876   0.0000
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 43.750000  13.3502  14.3502   0.0000  13.3502  14.3502   0.0000
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 44.500000  13.9710  14.9710   0.0000  13.9710  14.9710   0.0000
 44.750000  14.0178  15.0178   0.0001  14.0178  15.0178   0.0001
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 47.500000  15.5179  16.5179   0.0000  15.5179  16.5179   0.0000
 47.750000  15.1034  16.1034   0.0001  15.1034  16.1034   0.0001
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 48.750000  15.2094  16.2094   0.0001  15.2094  16.2094   0.0001
 49.000000  15.1168  16.1168   0.0001  15.1168  16.1168   0.0001
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 49.500000  16.2539  17.2539   0.0001  16.2539  17.2539   0.0001
 49.750000  16.3489  17.3489   0.0001  16.3489  17.3489   0.0001
 50.000000  15.0187  16.0187   0.0000  15.0187  16.0187   0.0000
 50.250000  16.3272  17.3272   0.0001  16.3272  17.3272   0.0001
 50.500000  16.0528  17.0528   0.0001  16.0528  17.0528   0.0001
 50.750000  16.4196  17.4196   0.0001  16.4196  17.4196   0.0001
 51.000000  16.8259  17.8259   0.0001  16.8259  17.8259   0.0001
 51.250000  15.5587  16.5587   0.0000  15.5587  16.5587   0.0000
 51.500000  16.3950  17.3950   0.0001  16.3950  17.3950   0.0001
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 52.000000  16.0925  17.0925   0.0001  16.0925  17.0925   0.0001
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 52.500000  17.1829  18.1829   0.0000  17.1829  18.1829   0.0000
 52.750000  17.5384  18.5384   0.0001  17.5384  18.5384   0.0001
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 88.500000  28.1172  29.1172   0.0001  28.1172  29.1172   0.0001
 88.750000  27.4677  28.4677   0.0001  27.4677  28.4677   0.0001
 89.000000  28.3160  29.3160   0.0000  28.3160  29.3160   0.0000
 89.250000  29.2626  30.2626   0.0000  29.2626  30.2626   0.0000
 89.500000  28.9803  29.9803   0.0001  28.9803  29.9803   0.0001
 89.750000  27.7864  28.7864   0.0001  27.7864  28.7864   0.0001
 90.000000  28.4074  29.4074   0.0001  28.4074  29.4074   0.0001
 90.250000  27.3048  28.3048   0.0001  27.3048  28.3048   0.0001
 90.500000  28.6134  29.6134   0.0001  28.6134  29.6134   0.0001
 90.750000  26.7885  27.7885   0.0001  26.7885  27.7885   0.0001
 91.000000  28.6276  29.6276   0.0001  28.6276  29.6276   0.0001
 91.250000  29.0343  30.0343   0.0000  29.0343  30.0343   0.0000
 91.500000  28.9067  29.9067   0.0000  28.9067  29.9067   0.0000
 91.750000  29.4537  30.4537   0.0000  29.4537  30.4537   0.0000
 92.000000  29.0662  30.0662   0.0001  29.0662  30.0662   0.0001
 92.250000  29.7005  30.7005   0.0001  29.7005  30.7005   0.0001
 92.500000  29.6141  30.6141   0.0001  29.6141  30.6141   0.0001
 92.750000  29.6393  30.6393   0.0000  29.6393  30.6393   0.0000
 93.000000  29.4964  30.4964   0.0001  29.4964  30.4964   0.0001
 93.250000  29.7888  30.7888   0.0001  29.7888  30.7888   0.0001
 93.500000  28.0586  29.0586   0.0001  28.0587  29.0587   0.0001
 93.750000  29.9872  30.9872   0.0001  29.9872  30.9872   0.0001
 94.000000  28.1782  29.1782   0.0001  28.1784  29.1784   0.0001
 94.250000  28.7693  29.7693   0.0001  28.7693  29.7693   0.0001
 94.500000  29.3541  30.3541   0.0000  29.3541  30.3541   0.0000
 94.750000  29.2034  30.2034   0.0000  29.2034  30.2034   0.0000
 95.000000  29.6254  30.6254   0.0001  29.6254  30.6254   0.0001
 95.250000  29.1481  30.1481   0.0000  29.1481  30.1481   0.0000
 95.500000  29.7590  30.7590   0.0000  29.7590  30.7590   0.0000
 95.750000  29.6971  30.6971   0.0000  29.6971  30.6971   0.0000
 96.000000  29.8248  30.8248   0.0001  29.8248  30.8248   0.0001
 96.250000  29.4804  30.4804   0.0001  29.4804  30.4804   0.0001
 96.500000  30.1150  31.1150   0.0001  30.1150  31.1150   0.0001
 96.750000  29.2877  30.2877   0.0001  29.2877  30.2877   0.0001
 97.000000  30.9275  31.9275   0.0001  30.9275  31.9275   0.0001
 97.250000  28.2932  29.2932   0.0001  28.2932  29.2932   0.0001
 97.500000  31.3549  32.3549   0.0001  31.3438  32.3438   0.0001
 97.750000  31.1175  32.1175   0.0000  31.1172  32.1172   0.0000
 98.000000  30.7921  31.7921   0.0001  30.7921  31.7921   0.0001
 98.250000  31.1990  32.1990   0.0001  31.1990  32.1990   0.0001
 98.500000  30.6488  31.6488   0.0001  30.6488  31.6488   0.0001
 98.750000  31.3462  32.3462   0.0000  31.3462  32.3462   0.0000
 99.000000  31.4013  32.4013   0.0000  31.4013  32.4013   0.0000
 99.250000  31.1480  32.1480   0.0000  31.1480  32.1480   0.0000
 99.500000  31.2079  32.2079   0.0000  31.2079  32.2079   0.0000
 99.750000  31.4616  32.4616   0.0001  31.4616  32.4616   0.0001
 100.000000  31.1434  32.1434   0.0001  31.1434  32.1434   0.0001
 100.250000  31.8777  32.8777   0.0001  31.8777  32.8777   0.0001
 100.500000  29.9216  30.9216   0.0001  29.9216  30.9216   0.0001
 100.750000  33.5430  34.5430   0.0001  33.5430  34.5430   0.0001
 101.000000  33.1555  34.1555   0.0000  33.1555  34.1555   0.0000
 101.250000  31.6932  32.6932   0.0000  31.6932  32.6932   0.0000
 101.500000  32.5199  33.5199   0.0001  32.5199  33.5199   0.0001
 101.750000  31.5930  32.5930   0.0001  31.5930  32.5930   0.0001
 102.000000  32.2981  33.2981   0.0000  32.2981  33.2981   0.0000
 102.250000  32.2886  33.2886   0.0000  32.2886  33.2886   0.0000
 102.500000  32.4482  33.4482   0.0001  32.4482  33.4482   0.0001
 102.750000  32.8988  33.8988   0.0001  32.8988  33.8988   0.0001
 103.000000  32.6250  33.6250   0.0001  32.6250  33.6250   0.0001
 103.250000  31.8492  32.8492   0.0001  31.8492  32.8492   0.0001
 103.500000  33.2489  34.2489   0.0001  33.2489  34.2489   0.0001
 103.750000  31.5151  32.5151   0.0001  31.5151  32.5151   0.0001
 104.000000  35.1123  36.1123   0.0001  34.9958  35.9958   0.0001
 104.250000  33.5786  34.5786   0.0000  33.5786  34.5786   0.0000
 104.500000  33.3743  34.3743   0.0000  33.3743  34.3743   0.0000
 104.750000  32.8565  33.8565   0.0001  32.8565  33.8565   0.0001
 105.000000  33.3878  34.3878   0.0000  33.3878  34.3878   0.0000
 105.250000  33.5407  34.5407   0.0001  33.5407  34.5407   0.0001
 105.500000  33.5782  34.5782   0.0001  33.5782  34.5782   0.0001
 105.750000  33.4424  34.4424   0.0001  33.4424  34.4424   0.0001
 106.000000  33.5877  34.5877   0.0000  33.5877  34.5877   0.0000
 106.250000  33.6673  34.6673   0.0001  33.6673  34.6673   0.0001
 106.500000  33.4228  34.4228   0.0001  33.4228  34.4228   0.0001
 106.750000  34.7414  35.7414   0.0001  34.7414  35.7414   0.0001
 107.000000  33.3332  34.3332   0.0001  33.3332  34.3332   0.0001
 107.250000  35.0870  36.0870   0.0001  35.0870  36.0870   0.0001
 107.500000  33.5445  34.5445   0.0001  33.5445  34.5445   0.0001
 107.750000  33.5552  34.5552   0.0000  33.5552  34.5552   0.0000
 108.000000  33.3770  34.3770   0.0000  33.3770  34.3770   0.0000
 108.250000  32.8967  33.8967   0.0001  32.8967  33.8967   0.0001
 108.500000  33.6200  34.6200   0.0001  33.6200  34.6200   0.0001
 108.750000  33.5640  34.5640   0.0001  33.5640  34.5640   0.0001
 109.000000  33.5274  34.5274   0.0000  33.5274  34.5274   0.0000
 109.250000  33.8522  34.8522   0.0000  33.8522  34.8522   0.0000
 109.500000  33.6961  34.6961   0.0001  33.6961  34.6961   0.0001
 109.750000  33.5290  34.5290   0.0000  33.5290  34.5290   0.0000
 110.000000  34.5353  35.5353   0.0001  34.5353  35.5353   0.0001
 110.250000  33.5084  34.5084   0.0001  33.5084  34.5084   0.0001
 110.500000  37.9057  38.9057   0.0001  36.9972  37.9972   0.0001
 110.750000  35.4568  36.4568   0.0001  35.4568  36.4568   0.0001
 111.000000  35.2015  36.2015   0.0001  35.2015  36.2015   0.0001
 111.250000  34.8816  35.8816   0.0001  34.8816  35.8816   0.0001
 111.500000  35.0138  36.0138   0.0001  35.0138  36.0138   0.0001
 111.750000  35.2748  36.2748   0.0001  35.2748  36.2748   0.0001
 112.000000  35.1521  36.1521   0.0000  35.1521  36.1521   0.0000
 112.250000  35.0458  36.0458   0.0001  35.0458  36.0458   0.0001
 112.500000  35.1097  36.1097   0.0001  35.1097  36.1097   0.0001
 112.750000  35.2703  36.2703   0.0000  35.2703  36.2703   0.0000
 113.000000  35.2164  36.2164   0.0000  35.2164  36.2164   0.0000
 113.250000  35.6830  36.6830   0.0000  35.6830  36.6830   0.0000
 113.500000  35.1352  36.1352   0.0001  35.1352  36.1352   0.0001
 113.750000  37.9694  38.9694   0.0001  37.9691  38.9691   0.0001
 114.000000  36.1329  37.1329   0.0000  36.1329  37.1329   0.0000
 114.250000  36.0489  37.0489   0.0001  36.0489  37.0489   0.0001
 114.500000  35.7678  36.7678   0.0001  35.7678  36.7678   0.0001
 114.750000  35.9607  36.9607   0.0000  35.9607  36.9607   0.0000
 115.000000  36.8600  37.8600   0.0001  36.8600  37.8600   0.0001
 115.250000  36.0576  37.0576   0.0001  36.0576  37.0576   0.0001
 115.500000  36.3707  37.3707   0.0001  36.3707  37.3707   0.0001
 115.750000  36.7418  37.7418   0.0000  36.7418  37.7418   0.0000
 116.000000  36.1698  37.1698   0.0000  36.1698  37.1698   0.0000
 116.250000  35.9551  36.9551   0.0000  35.9551  36.9551   0.0000
 116.500000  36.8455  37.8455   0.0000  36.8455  37.8455   0.0000
 116.750000  36.7463  37.7463   0.0001  36.7463  37.7463   0.0001
 117.000000  39.4013  40.4013   0.0001  38.9881  39.9881   0.0001
 117.250000  37.0099  38.0099   0.0001  37.0099  38.0099   0.0001
 117.500000  37.0492  38.0492   0.0001  37.0492  38.0492   0.0001
 117.750000  36.0642  37.0642   0.0000  36.0642  37.0642   0.0000
 118.000000  36.7462  37.7462   0.0000  36.7462  37.7462   0.0000
 118.250000  37.6375  38.6375   0.0001  37.6375  38.6375   0.0001
 118.500000  37.0123  38.0123   0.0001  37.0123  38.0123   0.0001
 118.750000  37.6777  38.6777   0.0001  37.6777  38.6777   0.0001
 119.000000  37.6633  38.6633   0.0001  37.6633  38.6633   0.0001
 119.250000  37.0775  38.0775   0.0000  37.0775  38.0775   0.0000
 119.500000  37.7632  38.7632   0.0000  37.7632  38.7632   0.0000
 119.750000  37.8503  38.8503   0.0001  37.8503  38.8503   0.0001
 120.000000  37.7380  38.7380   0.0001  37.7380  38.7380   0.0001
 120.250000  40.6057  41.6057   0.0001  40.6057  41.6057   0.0001
 120.500000  37.9875  38.9875   0.0001  37.9875  38.9875   0.0001
 120.750000  38.2308  39.2308   0.0001  38.2308  39.2308   0.0001
 121.000000  37.0110  38.0110   0.0000  37.0110  38.0110   0.0000
 121.250000  38.1251  39.1251   0.0001  38.1251  39.1251   0.0001
 121.500000  38.9580  39.9580   0.0000  38.9580  39.9580   0.0000
 121.750000  37.4896  38.4896   0.0001  37.4896  38.4896   0.0001
 122.000000  38.1362  39.1362   0.0001  38.1362  39.1362   0.0001
 122.250000  38.2823  39.2823   0.0000  38.2823  39.2823   0.0000
 122.500000  38.0283  39.0283   0.0000  38.0283  39.0283   0.0000
 122.750000  38.2731  39.2731   0.0000  38.2731  39.2731   0.0000
 123.000000  38.5351  39.5351   0.0000  38.5351  39.5351   0.0000
 123.250000  38.6889  39.6889   0.0001  38.6889  39.6889   0.0001
 123.500000  41.0177  42.0177   0.0001  41.0177  42.0177   0.0001
 123.750000  39.0327  40.0327   0.0001  39.0327  40.0327   0.0001
 124.000000  39.2150  40.2150   0.0001  39.2150  40.2150   0.0001
 124.250000  38.3662  39.3662   0.0001  38.3662  39.3662   0.0001
 124.500000  39.3881  40.3881   0.0001  39.3881  40.3881   0.0001
 124.750000  39.7801  40.7801   0.0000  39.7801  40.7801   0.0000
 125.000000  38.9521  39.9521   0.0000  38.9521  39.9521   0.0000
 125.250000  39.2335  40.2335   0.0000  39.2335  40.2335   0.0000
 125.500000  39.4236  40.4236   0.0001  39.4236  40.4236   0.0001
 125.750000  39.0332  40.0332   0.0001  39.0332  40.0332   0.0001
 126.000000  39.0309  40.0309   0.0000  39.0309  40.0309   0.0000
 126.250000  40.0990  41.0990   0.0000  40.0990  41.0990   0.0000
 126.500000  39.5974  40.5974   0.0001  39.5974  40.5974   0.0001
 126.750000  41.4831  42.4831   0.0001  41.4831  42.4831   0.0001
 127.000000  39.5779  40.5779   0.0001  39.5779  40.5779   0.0001
 127.250000  39.9957  40.9957   0.0000  39.9957  40.9957   0.0000
 127.500000  39.1887  40.1887   0.0001  39.1887  40.1887   0.0001
 127.750000  39.7603  40.7603   0.0000  39.7603  40.7603   0.0000
 128.000000  40.9212  41.9212   0.0001  40.9212  41.9212   0.0001
 128.250000  39.6202  40.6202   0.0000  39.6202  40.6202   0.0000
 128.500000  40.1471  41.1471   0.0000  40.1471  41.1471   0.0000
 128.750000  40.2331  41.2331   0.0001  40.2331  41.2331   0.0001
 129.000000  40.0902  41.0902   0.0001  40.0902  41.0902   0.0001
 129.250000  39.6322  40.6322   0.0000  39.6322  40.6322   0.0000
 129.500000  41.0105  42.0105   0.0000  41.0105  42.0105   0.0000
 129.750000  40.2607  41.2607   0.0001  40.2607  41.2607   0.0001
 130.000000  41.9895  42.9895   0.0001  41.9895  42.9895   0.0001
 130.250000  40.9519  41.9519   0.0001  40.9519  41.9519   0.0001
 130.500000  40.8069  41.8069   0.0001  40.8069  41.8069   0.0001
 130.750000  39.7650  40.7650   0.0001  39.7650  40.7650   0.0001
 131.000000  40.2980  41.2980   0.0001  40.2980  41.2980   0.0001
 131.250000  41.9747  42.9747   0.0001  41.9747  42.9747   0.0001
 131.500000  40.3756  41.3756   0.0000  40.3756  41.3756   0.0000
 131.750000  41.2743  42.2743   0.0001  41.2743  42.2743   0.0001
 132.000000  40.8975  41.8975   0.0001  40.8975  41.8975   0.0001
 132.250000  40.9555  41.9555   0.0001  40.9555  41.9555   0.0001
 132.500000  40.6201  41.6201   0.0000  40.6201  41.6201   0.0000
 132.750000  41.5831  42.5831   0.0001  41.5831  42.5831   0.0001
 133.000000  41.1452  42.1452   0.0000  41.1452  42.1452   0.0000
 133.250000  41.9675  42.9675   0.0001  41.9675  42.9675   0.0001
 133.500000  41.8360  42.8360   0.0001  41.8360  42.8360   0.0001
 133.750000  41.9216  42.9216   0.0000  41.9216  42.9216   0.0000
 134.000000  41.8315  42.8315   0.0001  41.8315  42.8315   0.0001
 134.250000  41.3247  42.3247   0.0001  41.3247  42.3247   0.0001
 134.500000  41.9998  42.9998   0.0001  41.9998  42.9998   0.0001
 134.750000  41.0553  42.0553   0.0001  41.0553  42.0553   0.0001
 135.000000  41.9978  42.9978   0.0001  41.9978  42.9978   0.0001
 135.250000  41.9695  42.9695   0.0000  41.9695  42.9695   0.0000
 135.500000  41.9529  42.9529   0.0001  41.9529  42.9529   0.0001
 135.750000  41.8093  42.8093   0.0000  41.8093  42.8093   0.0000
 136.000000  41.9968  42.9968   0.0001  41.9968  42.9968   0.0001
 136.250000  41.9985  42.9985   0.0001  41.9985  42.9985   0.0001
r2: READRead quantities from a colvar file. This action has hidden defaults. More details VALUESthe values to read from the file=p3.* FILEthe name of the file from which to read these quantities=
regtest/basic/rt41/input_colvar
Click here to see an extract from this file.
×

FILE: regtest/basic/rt41/input_colvar

#! FIELDS time p2.X p2.Y p2.zzz p3.X p3.Y p3.zzz
 0.000000   1.9434   2.9434   0.0001   1.9434   2.9434   0.0001
 0.250000   1.0090   2.0090   0.0001   1.0090   2.0090   0.0001
 0.500000   1.0579   2.0579   0.0001   1.0579   2.0579   0.0001
 0.750000   1.0331   2.0331   0.0000   1.0331   2.0331   0.0000
 1.000000   1.3768   2.3768   0.0001   1.3768   2.3768   0.0001
 1.250000   1.4149   2.4149   0.0000   1.4149   2.4149   0.0000
 1.500000   1.0652   2.0652   0.0001   1.0652   2.0652   0.0001
 1.750000   1.0157   2.0157   0.0000   1.0157   2.0157   0.0000
 2.000000   1.1453   2.1453   0.0001   1.1453   2.1453   0.0001
 2.250000   1.3270   2.3270   0.0000   1.3270   2.3270   0.0000
 2.500000   1.0513   2.0513   0.0000   1.0513   2.0513   0.0000
 2.750000   1.3269   2.3269   0.0000   1.3269   2.3269   0.0000
 3.000000   1.0317   2.0317   0.0001   1.0317   2.0317   0.0001
 3.250000   3.1167   4.1167   0.0001   3.1167   4.1167   0.0001
 3.500000   1.2525   2.2525   0.0001   1.2525   2.2525   0.0001
 3.750000   1.2615   2.2615   0.0001   1.2615   2.2615   0.0001
 4.000000   1.4116   2.4116   0.0001   1.4116   2.4116   0.0001
 4.250000   2.2825   3.2825   0.0001   2.2825   3.2825   0.0001
 4.500000   2.0832   3.0832   0.0000   2.0832   3.0832   0.0000
 4.750000   1.5973   2.5973   0.0001   1.5973   2.5973   0.0001
 5.000000   1.3261   2.3261   0.0001   1.3261   2.3261   0.0001
 5.250000   2.4515   3.4515   0.0001   2.4515   3.4515   0.0001
 5.500000   2.5412   3.5412   0.0001   2.5412   3.5412   0.0001
 5.750000   1.8538   2.8538   0.0000   1.8538   2.8538   0.0000
 6.000000   1.3933   2.3933   0.0001   1.3933   2.3933   0.0001
 6.250000   1.7948   2.7948   0.0000   1.7948   2.7948   0.0000
 6.500000   3.8916   4.8916   0.0001   3.8916   4.8916   0.0001
 6.750000   2.4106   3.4106   0.0001   2.4106   3.4106   0.0001
 7.000000   2.9130   3.9130   0.0000   2.9130   3.9130   0.0000
 7.250000   2.7856   3.7856   0.0000   2.7856   3.7856   0.0000
 7.500000   3.0248   4.0248   0.0001   3.0248   4.0248   0.0001
 7.750000   3.0256   4.0256   0.0001   3.0256   4.0256   0.0001
 8.000000   2.8465   3.8465   0.0001   2.8465   3.8465   0.0001
 8.250000   1.7385   2.7385   0.0001   1.7385   2.7385   0.0001
 8.500000   3.2267   4.2267   0.0001   3.2267   4.2267   0.0001
 8.750000   3.4119   4.4119   0.0000   3.4119   4.4119   0.0000
 9.000000   2.6281   3.6281   0.0000   2.6281   3.6281   0.0000
 9.250000   2.4505   3.4505   0.0001   2.4505   3.4505   0.0001
 9.500000   2.9935   3.9935   0.0001   2.9935   3.9935   0.0001
 9.750000   4.2826   5.2826   0.0001   4.2826   5.2826   0.0001
 10.000000   3.1900   4.1900   0.0001   3.1900   4.1900   0.0001
 10.250000   3.5456   4.5456   0.0000   3.5456   4.5456   0.0000
 10.500000   3.5451   4.5451   0.0000   3.5451   4.5451   0.0000
 10.750000   4.1587   5.1587   0.0001   4.1587   5.1587   0.0001
 11.000000   3.9178   4.9178   0.0000   3.9178   4.9178   0.0000
 11.250000   3.8826   4.8826   0.0001   3.8826   4.8826   0.0001
 11.500000   3.2615   4.2615   0.0001   3.2615   4.2615   0.0001
 11.750000   4.2869   5.2869   0.0001   4.2869   5.2869   0.0001
 12.000000   4.5757   5.5757   0.0000   4.5757   5.5757   0.0000
 12.250000   3.2142   4.2142   0.0000   3.2142   4.2142   0.0000
 12.500000   3.9086   4.9086   0.0001   3.9086   4.9086   0.0001
 12.750000   3.7618   4.7618   0.0001   3.7618   4.7618   0.0001
 13.000000   4.8157   5.8157   0.0001   4.8157   5.8157   0.0001
 13.250000   3.9568   4.9568   0.0001   3.9568   4.9568   0.0001
 13.500000   4.8524   5.8524   0.0000   4.8524   5.8524   0.0000
 13.750000   4.4105   5.4105   0.0000   4.4105   5.4105   0.0000
 14.000000   4.9450   5.9450   0.0001   4.9450   5.9450   0.0001
 14.250000   4.7719   5.7719   0.0001   4.7719   5.7719   0.0001
 14.500000   4.5365   5.5365   0.0001   4.5365   5.5365   0.0001
 14.750000   4.0972   5.0972   0.0001   4.0972   5.0972   0.0001
 15.000000   5.5554   6.5554   0.0001   5.5554   6.5554   0.0001
 15.250000   5.1352   6.1352   0.0001   5.1352   6.1352   0.0001
 15.500000   4.2067   5.2067   0.0000   4.2067   5.2067   0.0000
 15.750000   4.5249   5.5249   0.0001   4.5249   5.5249   0.0001
 16.000000   4.7725   5.7725   0.0001   4.7725   5.7725   0.0001
 16.250000   5.9837   6.9837   0.0001   5.9837   6.9837   0.0001
 16.500000   4.7753   5.7753   0.0000   4.7753   5.7753   0.0000
 16.750000   6.0804   7.0804   0.0001   6.0804   7.0804   0.0001
 17.000000   5.7243   6.7243   0.0000   5.7243   6.7243   0.0000
 17.250000   6.0755   7.0755   0.0001   6.0755   7.0755   0.0001
 17.500000   5.7907   6.7907   0.0000   5.7907   6.7907   0.0000
 17.750000   5.5556   6.5556   0.0001   5.5556   6.5556   0.0001
 18.000000   5.4734   6.4734   0.0001   5.4734   6.4734   0.0001
 18.250000   6.8349   7.8349   0.0001   6.8349   7.8349   0.0001
 18.500000   6.1115   7.1115   0.0001   6.1115   7.1115   0.0001
 18.750000   5.4763   6.4763   0.0001   5.4763   6.4763   0.0001
 19.000000   6.0577   7.0577   0.0000   6.0577   7.0577   0.0000
 19.250000   5.8285   6.8285   0.0001   5.8285   6.8285   0.0001
 19.500000   5.8165   6.8165   0.0001   5.8165   6.8165   0.0001
 19.750000   5.4695   6.4695   0.0000   5.4695   6.4695   0.0000
 20.000000   6.8811   7.8811   0.0000   6.8811   7.8811   0.0000
 20.250000   7.1282   8.1282   0.0000   7.1282   8.1282   0.0000
 20.500000   7.0992   8.0992   0.0001   7.0992   8.0992   0.0001
 20.750000   6.0105   7.0105   0.0001   6.0105   7.0105   0.0001
 21.000000   6.8671   7.8671   0.0000   6.8671   7.8671   0.0000
 21.250000   6.2864   7.2864   0.0001   6.2864   7.2864   0.0001
 21.500000   7.2471   8.2471   0.0000   7.2471   8.2471   0.0000
 21.750000   7.2481   8.2481   0.0000   7.2481   8.2481   0.0000
 22.000000   5.9782   6.9782   0.0001   5.9782   6.9782   0.0001
 22.250000   6.8523   7.8523   0.0001   6.8523   7.8523   0.0001
 22.500000   6.8326   7.8326   0.0001   6.8326   7.8326   0.0001
 22.750000   6.5175   7.5175   0.0000   6.5175   7.5175   0.0000
 23.000000   6.4000   7.4000   0.0000   6.4000   7.4000   0.0000
 23.250000   8.0028   9.0028   0.0000   8.0028   9.0028   0.0000
 23.500000   8.1695   9.1695   0.0000   8.1695   9.1695   0.0000
 23.750000   7.9851   8.9851   0.0001   7.9851   8.9851   0.0001
 24.000000   6.8908   7.8908   0.0001   6.8908   7.8908   0.0001
 24.250000   7.4686   8.4686   0.0001   7.4686   8.4686   0.0001
 24.500000   7.0070   8.0070   0.0001   7.0070   8.0070   0.0001
 24.750000   8.5092   9.5092   0.0001   8.5092   9.5092   0.0001
 25.000000   8.1518   9.1518   0.0000   8.1518   9.1518   0.0000
 25.250000   7.3926   8.3926   0.0001   7.3926   8.3926   0.0001
 25.500000   7.9078   8.9078   0.0001   7.9078   8.9078   0.0001
 25.750000   7.3901   8.3901   0.0001   7.3901   8.3901   0.0001
 26.000000   7.5108   8.5108   0.0000   7.5108   8.5108   0.0000
 26.250000   7.3993   8.3993   0.0000   7.3993   8.3993   0.0000
 26.500000   9.0054  10.0054   0.0000   9.0054  10.0054   0.0000
 26.750000   9.0212  10.0212   0.0001   9.0212  10.0212   0.0001
 27.000000   9.2067  10.2067   0.0000   9.2067  10.2067   0.0000
 27.250000   7.3974   8.3974   0.0001   7.3974   8.3974   0.0001
 27.500000   8.4983   9.4983   0.0000   8.4983   9.4983   0.0000
 27.750000   8.4074   9.4074   0.0001   8.4074   9.4074   0.0001
 28.000000   9.4812  10.4812   0.0000   9.4812  10.4812   0.0000
 28.250000   8.9480   9.9480   0.0000   8.9480   9.9480   0.0000
 28.500000   8.8156   9.8156   0.0001   8.8156   9.8156   0.0001
 28.750000   9.3383  10.3383   0.0001   9.3383  10.3383   0.0001
 29.000000   8.6766   9.6766   0.0001   8.6766   9.6766   0.0001
 29.250000   8.8167   9.8167   0.0001   8.8167   9.8167   0.0001
 29.500000   8.8586   9.8586   0.0000   8.8586   9.8586   0.0000
 29.750000   9.7681  10.7681   0.0000   9.7681  10.7681   0.0000
 30.000000  10.1206  11.1206   0.0000  10.1206  11.1206   0.0000
 30.250000  10.2048  11.2048   0.0000  10.2048  11.2048   0.0000
 30.500000   8.8600   9.8600   0.0000   8.8600   9.8600   0.0000
 30.750000   9.2746  10.2746   0.0000   9.2746  10.2746   0.0000
 31.000000   9.5056  10.5056   0.0001   9.5056  10.5056   0.0001
 31.250000  10.3959  11.3959   0.0000  10.3959  11.3959   0.0000
 31.500000  10.0084  11.0084   0.0001  10.0084  11.0084   0.0001
 31.750000   9.8521  10.8521   0.0000   9.8521  10.8521   0.0000
 32.000000  10.3120  11.3120   0.0001  10.3120  11.3120   0.0001
 32.250000   9.5696  10.5696   0.0001   9.5696  10.5696   0.0001
 32.500000  10.2229  11.2229   0.0001  10.2229  11.2229   0.0001
 32.750000   9.2246  10.2246   0.0000   9.2246  10.2246   0.0000
 33.000000  11.0408  12.0408   0.0000  11.0408  12.0408   0.0000
 33.250000  10.9355  11.9355   0.0001  10.9355  11.9355   0.0001
 33.500000  11.0212  12.0212   0.0001  11.0212  12.0212   0.0001
 33.750000   9.9950  10.9950   0.0000   9.9950  10.9950   0.0000
 34.000000  10.8371  11.8371   0.0000  10.8371  11.8371   0.0000
 34.250000  10.7630  11.7630   0.0000  10.7630  11.7630   0.0000
 34.500000  11.3749  12.3749   0.0000  11.3749  12.3749   0.0000
 34.750000  10.8268  11.8268   0.0000  10.8268  11.8268   0.0000
 35.000000  10.9254  11.9254   0.0001  10.9254  11.9254   0.0001
 35.250000  11.4695  12.4695   0.0001  11.4695  12.4695   0.0001
 35.500000  10.3754  11.3754   0.0001  10.3754  11.3754   0.0001
 35.750000  11.2141  12.2141   0.0001  11.2141  12.2141   0.0001
 36.000000  10.9006  11.9006   0.0001  10.9006  11.9006   0.0001
 36.250000  12.3187  13.3187   0.0000  12.3187  13.3187   0.0000
 36.500000  12.0581  13.0581   0.0001  12.0581  13.0581   0.0001
 36.750000  12.1095  13.1095   0.0001  12.1095  13.1095   0.0001
 37.000000  10.9742  11.9742   0.0000  10.9742  11.9742   0.0000
 37.250000  11.5190  12.5190   0.0000  11.5190  12.5190   0.0000
 37.500000  11.6730  12.6730   0.0001  11.6730  12.6730   0.0001
 37.750000  12.7361  13.7361   0.0001  12.7361  13.7361   0.0001
 38.000000  12.1409  13.1409   0.0001  12.1409  13.1409   0.0001
 38.250000  12.3599  13.3599   0.0000  12.3599  13.3599   0.0000
 38.500000  12.3989  13.3989   0.0001  12.3989  13.3989   0.0001
 38.750000  11.1104  12.1104   0.0001  11.1104  12.1104   0.0001
 39.000000  11.8881  12.8881   0.0001  11.8881  12.8881   0.0001
 39.250000  11.8041  12.8041   0.0000  11.8041  12.8041   0.0000
 39.500000  13.5494  14.5494   0.0000  13.5494  14.5494   0.0000
 39.750000  13.2306  14.2306   0.0001  13.2306  14.2306   0.0001
 40.000000  13.4767  14.4767   0.0001  13.4767  14.4767   0.0001
 40.250000  12.1017  13.1017   0.0000  12.1017  13.1017   0.0000
 40.500000  12.7382  13.7382   0.0000  12.7382  13.7382   0.0000
 40.750000  13.0408  14.0408   0.0001  13.0408  14.0408   0.0001
 41.000000  13.6144  14.6144   0.0001  13.6144  14.6144   0.0001
 41.250000  12.9117  13.9117   0.0001  12.9117  13.9117   0.0001
 41.500000  12.9911  13.9911   0.0000  12.9911  13.9911   0.0000
 41.750000  13.9208  14.9208   0.0001  13.9208  14.9208   0.0001
 42.000000  12.6076  13.6076   0.0001  12.6076  13.6076   0.0001
 42.250000  12.7982  13.7982   0.0001  12.7982  13.7982   0.0001
 42.500000  12.8370  13.8370   0.0000  12.8370  13.8370   0.0000
 42.750000  14.3876  15.3876   0.0000  14.3876  15.3876   0.0000
 43.000000  14.4720  15.4720   0.0001  14.4720  15.4720   0.0001
 43.250000  14.6719  15.6719   0.0001  14.6719  15.6719   0.0001
 43.500000  12.8227  13.8227   0.0000  12.8227  13.8227   0.0000
 43.750000  13.3502  14.3502   0.0000  13.3502  14.3502   0.0000
 44.000000  13.8173  14.8173   0.0001  13.8173  14.8173   0.0001
 44.250000  14.8745  15.8745   0.0000  14.8745  15.8745   0.0000
 44.500000  13.9710  14.9710   0.0000  13.9710  14.9710   0.0000
 44.750000  14.0178  15.0178   0.0001  14.0178  15.0178   0.0001
 45.000000  14.5201  15.5201   0.0001  14.5201  15.5201   0.0001
 45.250000  13.1381  14.1381   0.0001  13.1381  14.1381   0.0001
 45.500000  14.5934  15.5934   0.0001  14.5934  15.5934   0.0001
 45.750000  13.4843  14.4843   0.0001  13.4843  14.4843   0.0001
 46.000000  15.4321  16.4321   0.0000  15.4321  16.4321   0.0000
 46.250000  15.4231  16.4231   0.0000  15.4231  16.4231   0.0000
 46.500000  15.6806  16.6806   0.0001  15.6806  16.6806   0.0001
 46.750000  13.9386  14.9386   0.0000  13.9386  14.9386   0.0000
 47.000000  14.5064  15.5064   0.0000  14.5064  15.5064   0.0000
 47.250000  14.9508  15.9508   0.0001  14.9508  15.9508   0.0001
 47.500000  15.5179  16.5179   0.0000  15.5179  16.5179   0.0000
 47.750000  15.1034  16.1034   0.0001  15.1034  16.1034   0.0001
 48.000000  14.9114  15.9114   0.0001  14.9114  15.9114   0.0001
 48.250000  15.5412  16.5412   0.0002  15.5412  16.5412   0.0002
 48.500000  14.3423  15.3423   0.0001  14.3423  15.3423   0.0001
 48.750000  15.2094  16.2094   0.0001  15.2094  16.2094   0.0001
 49.000000  15.1168  16.1168   0.0001  15.1168  16.1168   0.0001
 49.250000  15.9575  16.9575   0.0000  15.9575  16.9575   0.0000
 49.500000  16.2539  17.2539   0.0001  16.2539  17.2539   0.0001
 49.750000  16.3489  17.3489   0.0001  16.3489  17.3489   0.0001
 50.000000  15.0187  16.0187   0.0000  15.0187  16.0187   0.0000
 50.250000  16.3272  17.3272   0.0001  16.3272  17.3272   0.0001
 50.500000  16.0528  17.0528   0.0001  16.0528  17.0528   0.0001
 50.750000  16.4196  17.4196   0.0001  16.4196  17.4196   0.0001
 51.000000  16.8259  17.8259   0.0001  16.8259  17.8259   0.0001
 51.250000  15.5587  16.5587   0.0000  15.5587  16.5587   0.0000
 51.500000  16.3950  17.3950   0.0001  16.3950  17.3950   0.0001
 51.750000  15.2996  16.2996   0.0001  15.2996  16.2996   0.0001
 52.000000  16.0925  17.0925   0.0001  16.0925  17.0925   0.0001
 52.250000  16.4335  17.4335   0.0001  16.4335  17.4335   0.0001
 52.500000  17.1829  18.1829   0.0000  17.1829  18.1829   0.0000
 52.750000  17.5384  18.5384   0.0001  17.5384  18.5384   0.0001
 53.000000  17.2631  18.2631   0.0001  17.2631  18.2631   0.0001
 53.250000  16.2614  17.2614   0.0001  16.2614  17.2614   0.0001
 53.500000  17.0032  18.0032   0.0000  17.0032  18.0032   0.0000
 53.750000  17.5027  18.5027   0.0001  17.5027  18.5027   0.0001
 54.000000  17.0522  18.0522   0.0001  17.0522  18.0522   0.0001
 54.250000  17.3532  18.3532   0.0001  17.3532  18.3532   0.0001
 54.500000  16.6059  17.6059   0.0000  16.6059  17.6059   0.0000
 54.750000  16.9281  17.9281   0.0001  16.9281  17.9281   0.0001
 55.000000  15.7926  16.7926   0.0001  15.7926  16.7926   0.0001
 55.250000  17.2110  18.2110   0.0000  17.2110  18.2110   0.0000
 55.500000  17.5846  18.5846   0.0001  17.5846  18.5846   0.0001
 55.750000  17.8666  18.8666   0.0001  17.8666  18.8666   0.0001
 56.000000  18.2468  19.2468   0.0001  18.2468  19.2468   0.0001
 56.250000  18.1218  19.1218   0.0001  18.1218  19.1218   0.0001
 56.500000  16.9705  17.9705   0.0001  16.9705  17.9705   0.0001
 56.750000  17.7506  18.7506   0.0000  17.7506  18.7506   0.0000
 57.000000  18.1285  19.1285   0.0001  18.1285  19.1285   0.0001
 57.250000  18.0247  19.0247   0.0001  18.0247  19.0247   0.0001
 57.500000  18.0924  19.0924   0.0001  18.0924  19.0924   0.0001
 57.750000  17.9847  18.9847   0.0001  17.9847  18.9847   0.0001
 58.000000  17.8135  18.8135   0.0001  17.8135  18.8135   0.0001
 58.250000  17.0656  18.0656   0.0001  17.0656  18.0656   0.0001
 58.500000  17.6905  18.6905   0.0001  17.6905  18.6905   0.0001
 58.750000  18.5188  19.5188   0.0001  18.5188  19.5188   0.0001
 59.000000  18.9824  19.9824   0.0000  18.9824  19.9824   0.0000
 59.250000  19.1426  20.1426   0.0000  19.1426  20.1426   0.0000
 59.500000  19.0595  20.0595   0.0001  19.0595  20.0595   0.0001
 59.750000  18.7700  19.7700   0.0001  18.7700  19.7700   0.0001
 60.000000  19.5301  20.5301   0.0000  19.5301  20.5301   0.0000
 60.250000  19.3457  20.3457   0.0001  19.3457  20.3457   0.0001
 60.500000  19.0527  20.0527   0.0000  19.0527  20.0527   0.0000
 60.750000  19.1799  20.1799   0.0001  19.1799  20.1799   0.0001
 61.000000  18.9106  19.9106   0.0000  18.9106  19.9106   0.0000
 61.250000  18.8817  19.8817   0.0001  18.8817  19.8817   0.0001
 61.500000  18.0910  19.0910   0.0001  18.0910  19.0910   0.0001
 61.750000  19.0315  20.0315   0.0001  19.0315  20.0315   0.0001
 62.000000  19.4761  20.4761   0.0001  19.4761  20.4761   0.0001
 62.250000  19.6156  20.6156   0.0001  19.6156  20.6156   0.0001
 62.500000  20.5450  21.5450   0.0000  20.5450  21.5450   0.0000
 62.750000  19.5918  20.5918   0.0001  19.5918  20.5918   0.0001
 63.000000  19.4211  20.4211   0.0001  19.4211  20.4211   0.0001
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 63.500000  20.5284  21.5284   0.0001  20.5284  21.5284   0.0001
 63.750000  19.3983  20.3983   0.0001  19.3983  20.3983   0.0001
 64.000000  20.0183  21.0183   0.0001  20.0183  21.0183   0.0001
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 64.500000  19.9145  20.9145   0.0002  19.9145  20.9145   0.0002
 64.750000  18.8479  19.8479   0.0000  18.8479  19.8479   0.0000
 65.000000  20.1734  21.1734   0.0001  20.1734  21.1734   0.0001
 65.250000  20.7230  21.7230   0.0000  20.7230  21.7230   0.0000
 65.500000  20.9771  21.9771   0.0000  20.9771  21.9771   0.0000
 65.750000  21.4568  22.4568   0.0000  21.4568  22.4568   0.0000
 66.000000  20.5483  21.5483   0.0001  20.5483  21.5483   0.0001
 66.250000  20.9015  21.9015   0.0001  20.9015  21.9015   0.0001
 66.500000  21.1926  22.1926   0.0000  21.1926  22.1926   0.0000
 66.750000  21.3126  22.3126   0.0001  21.3126  22.3126   0.0001
 67.000000  20.2389  21.2389   0.0001  20.2389  21.2389   0.0001
 67.250000  20.7179  21.7179   0.0001  20.7179  21.7179   0.0001
 67.500000  20.4320  21.4320   0.0000  20.4320  21.4320   0.0000
 67.750000  21.0638  22.0638   0.0001  21.0638  22.0638   0.0001
 68.000000  19.9730  20.9730   0.0001  19.9730  20.9730   0.0001
 68.250000  21.5699  22.5699   0.0001  21.5699  22.5699   0.0001
 68.500000  21.6000  22.6000   0.0000  21.6000  22.6000   0.0000
 68.750000  21.6405  22.6405   0.0000  21.6405  22.6405   0.0000
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 69.250000  21.1910  22.1910   0.0001  21.1910  22.1910   0.0001
 69.500000  21.6420  22.6420   0.0001  21.6420  22.6420   0.0001
 69.750000  22.0399  23.0399   0.0000  22.0399  23.0399   0.0000
 70.000000  22.1538  23.1538   0.0001  22.1538  23.1538   0.0001
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 70.500000  22.1667  23.1667   0.0001  22.1667  23.1667   0.0001
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 71.000000  22.1309  23.1309   0.0001  22.1309  23.1309   0.0001
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 131.750000  41.2743  42.2743   0.0001  41.2743  42.2743   0.0001
 132.000000  40.8975  41.8975   0.0001  40.8975  41.8975   0.0001
 132.250000  40.9555  41.9555   0.0001  40.9555  41.9555   0.0001
 132.500000  40.6201  41.6201   0.0000  40.6201  41.6201   0.0000
 132.750000  41.5831  42.5831   0.0001  41.5831  42.5831   0.0001
 133.000000  41.1452  42.1452   0.0000  41.1452  42.1452   0.0000
 133.250000  41.9675  42.9675   0.0001  41.9675  42.9675   0.0001
 133.500000  41.8360  42.8360   0.0001  41.8360  42.8360   0.0001
 133.750000  41.9216  42.9216   0.0000  41.9216  42.9216   0.0000
 134.000000  41.8315  42.8315   0.0001  41.8315  42.8315   0.0001
 134.250000  41.3247  42.3247   0.0001  41.3247  42.3247   0.0001
 134.500000  41.9998  42.9998   0.0001  41.9998  42.9998   0.0001
 134.750000  41.0553  42.0553   0.0001  41.0553  42.0553   0.0001
 135.000000  41.9978  42.9978   0.0001  41.9978  42.9978   0.0001
 135.250000  41.9695  42.9695   0.0000  41.9695  42.9695   0.0000
 135.500000  41.9529  42.9529   0.0001  41.9529  42.9529   0.0001
 135.750000  41.8093  42.8093   0.0000  41.8093  42.8093   0.0000
 136.000000  41.9968  42.9968   0.0001  41.9968  42.9968   0.0001
 136.250000  41.9985  42.9985   0.0001  41.9985  42.9985   0.0001
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=r1.X,r2.* FILEthe name of the file on which to output these quantities=colvar

Notice that the READ command preseves the part of the name that appears after the ".". Consequently, when we read the value p2.X from the input file the output value the action with label r1 calls the output value that contains this information r1.X. The READ command is implemented this way so that you can use the wildcard syntax that is illustrated in the command labelled r2 in the above input.

Reading COLVAR files and trajectories

The example input below indicates a case where a trajectory is being post processed and where some COLVAR files that were generated when the MD simulation was run are read in.

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS INPUTFILES=regtest/basic/rt19/input_colvar2
# The distance here is being calculated from the trajectory
d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
# This CV is being read in from a file that was output with the same frequency as frames
# were output from the trajectory. Notice that you can read from zip files
r1: READRead quantities from a colvar file. This action has hidden defaults. More details VALUESthe values to read from the file=rmsd0  FILEthe name of the file from which to read these quantities=regtest/basic/rt19/input_colvar.gz
# This CV is being read in from a file that was output with twice as frequency as frames
r2: READRead quantities from a colvar file. This action has hidden defaults. More details VALUESthe values to read from the file=rmsd0  FILEthe name of the file from which to read these quantities=
regtest/basic/rt19/input_colvar2
Click here to see an extract from this file.
×

FILE: regtest/basic/rt19/input_colvar2

#! FIELDS time rmsd0 rmsds0 rmsd1 rmsds1 rmsd2 rmsds2 rmsd3 rmsds3 rmsd4 rmsds4 sum @11.bias @11.force2
 0.000000  1.496  1.643  1.496  1.643  1.337  1.486  1.336  1.486  2.329  2.130 16.381  6.550 13.100
 0.050000  1.502  1.650  1.503  1.650  1.347  1.497  1.347  1.496  2.332  2.128 16.452  6.294 12.589
 0.100000  1.503  1.653  1.504  1.653  1.351  1.502  1.350  1.501  2.324  2.120 16.461  6.262 12.525
 0.150000  1.502  1.653  1.502  1.654  1.350  1.503  1.350  1.503  2.308  2.108 16.433  6.361 12.721
 0.200000  1.496  1.649  1.496  1.649  1.347  1.500  1.346  1.499  2.278  2.080 16.340  6.696 13.392
 0.000000  1.496  1.643  1.496  1.643  1.337  1.486  1.336  1.486  2.329  2.130 16.381  6.550 13.100
 0.050000  1.502  1.650  1.503  1.650  1.347  1.497  1.347  1.496  2.332  2.128 16.452  6.294 12.589
 0.100000  1.503  1.653  1.504  1.653  1.351  1.502  1.350  1.501  2.324  2.120 16.461  6.262 12.525
 0.150000  1.502  1.653  1.502  1.654  1.350  1.503  1.350  1.503  2.308  2.108 16.433  6.361 12.721
 0.200000  1.496  1.649  1.496  1.649  1.347  1.500  1.346  1.499  2.278  2.080 16.340  6.696 13.392
EVERY only read every nth line of the colvar file=2 IGNORE_TIME ignore the time in the colvar file
# This outputs our three quantities PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d,r1,r2 FILEthe name of the file on which to output these quantities=colvar

The driver command to run this script as follows:

plumed driver --plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz

When you are doing analyses like these, which involve mixing using READ command and analysing a trajectory, PLUMED forces you to take care to ensure that everything in the input file was generated from the same step in the input trajectory. You must use the --trajectory-stride and --timestep commands when using driver above so PLUMED can correctly calculate the simulation time and compare it with the time stamps in any colvar files that are being read in using READ commands.

If you want to turn off these checks either because you are confident that you have set things up correctly or if you are not mixing variables that have been calculated from a trajectory with variables that are being read from a file you can use the IGNORE_TIME flag. Notice also that you can use the EVERY flag to tell PLUMED to ignore parts of the COLVAR file if data has been output to that file more frequently that data has been output to the trajectory.

Syntax

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
STRIDE compulsory 1 the frequency with which the file should be read
EVERY compulsory 1 only read every nth line of the colvar file
VALUES compulsory none the values to read from the file
FILE compulsory none the name of the file from which to read these quantities
IGNORE_TIME optional false ignore the time in the colvar file
IGNORE_FORCES optional false use this flag if the forces added by any bias can be safely ignored
UPDATE_FROM optional not used Only update this action from this time
UPDATE_UNTIL optional not used Only update this action until this time