Project ID: plumID:23.024
Source: examples/driverTests/plumed_C45.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.9
tested onmaster
tested on master
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../../src/pines/PINES.cpp
LOAD
Loads a library, possibly defining new actions. More details
FILE
file to be loaded
=../../src/annbfunc/ANNB.cpp
PINES
This action is not part of PLUMED and was included by using a LOAD command More details
... LABEL=pines PRECISION=10000 NLIST ONLYCROSS REF_FILE=../SimulationFiles/C45/md.pdb PINESATOMS=10 ATOMTYPES=C3,C8,C13,C18,C23,C28,C33,C38,C43,OW SFACTOR=1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0 SORT=1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0 SWITCH1={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH2={RATIONAL R_0=0.83 MM=12 NN=6} SWITCH3={RATIONAL R_0=0.82 MM=12 NN=6} SWITCH4={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH5={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH6={RATIONAL R_0=0.76 MM=12 NN=6} SWITCH7={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH8={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH9={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH10={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH11={RATIONAL R_0=0.83 MM=12 NN=6} SWITCH12={RATIONAL R_0=0.82 MM=12 NN=6} SWITCH13={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH14={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH15={RATIONAL R_0=0.76 MM=12 NN=6} SWITCH16={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH17={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH18={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH19={RATIONAL R_0=0.83 MM=12 NN=6} SWITCH20={RATIONAL R_0=0.82 MM=12 NN=6} SWITCH21={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH22={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH23={RATIONAL R_0=0.76 MM=12 NN=6} SWITCH24={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH25={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH26={RATIONAL R_0=0.83 MM=12 NN=6} SWITCH27={RATIONAL R_0=0.82 MM=12 NN=6} SWITCH28={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH29={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH30={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH31={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH32={RATIONAL R_0=0.83 MM=12 NN=6} SWITCH33={RATIONAL R_0=0.82 MM=12 NN=6} SWITCH34={RATIONAL R_0=0.77 MM=12 NN=6} SWITCH35={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH36={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH37={RATIONAL R_0=0.83 MM=12 NN=6} SWITCH38={RATIONAL R_0=0.82 MM=12 NN=6} SWITCH39={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH40={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH41={RATIONAL R_0=0.83 MM=12 NN=6} SWITCH42={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH43={RATIONAL R_0=0.55 MM=28 NN=14} SWITCH44={RATIONAL R_0=0.52 MM=8 NN=4} SWITCH45={RATIONAL R_0=0.52 MM=8 NN=4} NL_CUTOFF=6.0,6.0,6.0,6.0,6.0,6.0,6.0,6.0,0.8,6.0,6.0,6.0,6.0,6.0,6.0,6.0,0.8,6.0,6.0,6.0,6.0,6.0,6.0,0.8,6.0,6.0,6.0,6.0,6.0,0.8,6.0,6.0,6.0,6.0,0.8,6.0,6.0,6.0,0.8,6.0,6.0,0.8,6.0,0.8,0.8 NL_STRIDE=20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0,20.0 NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1 NL_CONSTANT_SIZE=8 ... PINES
ANNB
This action is not part of PLUMED and was included by using a LOAD command More details
... LABEL=ann ARG=pines NUM_LAYERS=6 NUM_NODES=108,64,32,16,3,3 ACTIVATIONS=BNTanh,BNTanh,BNTanh,BNTanh,Linear 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WEIGHTS3=0.081952,-0.113561,-0.106991,-0.100496,-0.114124,0.147047,-0.096382,0.024912,-0.051522,0.039425,-0.243182,-0.238101,0.181701,-0.148554,0.047988,0.102114,0.013047,0.075074,0.115139,-0.218336,-0.230011,0.099058,0.177794,-0.109544,0.156298,-0.054906,0.114081,-0.197845,-0.063079,0.030837,0.038690,0.138948,-0.135155,0.221357,-0.124309,-0.094124,-0.227247,0.210987,0.068937,0.013569,0.139156,0.051611,0.026849,0.074956,0.000530,-0.140631,-0.073593,0.117326 WEIGHTS4=-0.66096485,-0.74776804,-0.06299518,0.2665534,-0.3124232,0.91177905,-0.70148045,0.5858623,0.40582088 BIASES0=0.032801,-0.143684,-0.021009,-0.380668,-0.057963,-0.107947,-0.233673,0.135863,0.063363,-0.442359,0.623385,-0.104422,-0.448285,0.166030,0.416202,-0.055978,-0.523833,0.141584,-0.108598,-0.250646,0.168256,-0.060080,0.152130,-0.423754,0.034958,0.048731,-0.348825,-0.053679,-0.034020,-0.025327,-0.064084,-0.093109,0.171287,-0.297482,0.124922,0.209352,-0.276976,-0.361541,-0.277277,0.368077,-0.039569,-0.422276,-0.254422,-0.299995,-0.013696,-0.241852,-0.483466,-0.060324,-0.117433,0.103795,-0.270748,-0.082667,0.112888,0.280880,-0.084352,0.243720,-0.077836,-0.247886,0.134471,-0.162210,0.402733,0.015544,-0.128889,0.271724 BIASES1=-0.007666,0.137912,-0.180594,-0.075688,0.000963,-0.281666,0.052436,-0.535955,-0.182493,-0.092969,-0.143102,-0.079913,-0.040741,0.069422,0.297928,0.067462,-0.311515,-0.044571,0.102368,0.024922,0.303596,-0.206238,0.014413,0.334354,-0.179291,-0.147012,-0.109733,-0.108316,-0.145324,-0.323307,-0.123722,-0.173468 BIASES2=0.032858,-0.029546,-0.300497,-0.064017,0.202538,-0.114526,-0.016999,0.289620,-0.227093,0.109906,-0.131327,-0.352293,0.166492,0.188653,-0.390345,0.107689 BIASES3=0.167351,-0.146972,-0.096695 BIASES4=0.0,0.0,0.0 GAMMAS0=0.976467,1.014736,1.024274,1.024030,0.973907,0.941647,1.008141,1.015756,0.963140,1.098595,1.060797,0.990187,1.076473,0.973387,0.980352,0.976326,1.007635,1.006972,1.011513,1.015473,0.968924,0.974061,0.975782,1.024817,1.022339,1.024198,1.032006,0.967627,0.987648,0.981576,1.047892,0.971956,0.999653,1.034942,1.006507,0.971679,0.989016,1.032176,1.047114,1.001426,0.985158,1.069139,1.017969,1.033562,1.045781,0.981387,1.115233,0.990136,1.028930,1.007463,0.977405,0.999063,1.012563,0.922016,0.939417,0.960165,0.958586,1.015976,1.014120,0.987054,1.021266,0.981551,1.030082,0.951681 GAMMAS1=0.969875,0.997327,0.999775,1.014646,0.951825,0.963904,1.010644,1.012652,1.018017,0.998044,0.990578,0.956107,0.991446,0.965635,1.013937,0.965425,0.983212,1.004241,0.985907,0.981737,1.019184,0.967558,1.000038,0.972848,0.998885,1.010913,0.982807,0.963606,0.989873,0.994115,0.934289,0.993109 GAMMAS2=1.010873,0.960714,0.983116,0.945268,0.971458,0.960262,0.981657,0.968717,0.996350,0.984015,1.005104,0.980263,0.981917,0.934285,1.005277,0.945230 GAMMAS3=0.968659,0.973541,0.962177 BETAS0=0.140731,0.200388,0.165030,-0.033018,-0.666952,0.247582,-0.178459,-0.107798,0.014802,0.071256,-0.060250,-0.062470,-0.247035,-0.139130,0.469338,0.133960,-0.250666,0.018061,0.213000,0.147354,-0.285102,0.009010,-0.249284,-0.107493,0.128669,0.377989,0.162303,0.299463,0.458330,0.337053,0.098399,0.121322,-0.226751,-0.246761,-0.036270,0.158265,0.071748,-0.278125,0.133013,-0.107441,0.360458,0.091205,0.466346,0.032285,-0.170594,-0.075758,-0.321418,-0.060543,-0.135063,-0.026158,-0.090272,-0.005994,0.299345,0.331273,-0.419660,0.136765,-0.067227,-0.140214,-0.029444,-0.186845,0.238347,-0.124558,0.152875,0.226307 BETAS1=-0.074761,0.029015,-0.028666,-0.050880,-0.165329,0.171397,0.441165,-0.028835,0.105393,-0.001436,0.475037,-0.050675,-0.183977,0.091079,-0.000234,0.028719,-0.059839,0.191183,0.101236,0.065734,0.013250,0.076499,0.161359,-0.206747,0.105033,0.021850,0.317233,0.000819,0.160278,-0.099542,0.254946,-0.252365 BETAS2=-0.045969,0.061953,0.041706,-0.035914,-0.036773,0.009090,0.076432,-0.043361,0.070494,-0.048334,0.067991,0.008526,-0.068653,0.029594,-0.026703,0.024502 BETAS3=0.000988,0.004475,0.000592 EXPECTATIONS0=-0.036160,-0.664331,-0.603082,-0.967311,0.310029,-0.649840,-0.677908,0.791995,-0.288191,-0.952435,0.966223,-0.784965,-0.950693,0.909756,0.844045,-0.610989,-0.929918,0.848763,-0.723842,-0.791697,-0.106989,0.082001,0.707041,-0.921343,-0.401348,-0.648901,-0.959415,-0.611419,-0.290593,-0.444404,-0.326771,-0.127447,0.829796,-0.909642,0.478722,0.787649,-0.825211,-0.847404,-0.945283,0.957640,-0.693651,-0.910126,-0.855876,-0.940081,-0.144846,-0.902685,-0.987389,-0.445739,-0.375685,-0.300575,-0.792538,-0.379009,-0.070510,0.827535,-0.741364,0.771333,-0.580649,-0.755752,0.750839,-0.322819,0.899043,-0.134533,-0.649715,0.729224 EXPECTATIONS1=0.142629,0.008375,-0.514738,-0.165286,0.039738,-0.486941,0.225692,-0.718683,-0.085600,-0.101371,-0.066320,-0.330227,0.238683,0.171668,0.443133,0.209550,-0.428078,0.190817,-0.051277,-0.001319,0.342618,-0.230872,0.049068,0.468650,-0.305318,-0.082837,0.010200,-0.121822,-0.207587,-0.462596,-0.192222,-0.226812 EXPECTATIONS2=-0.073289,0.056012,-0.494017,-0.204047,0.228290,-0.157394,0.091766,0.247539,-0.290336,0.064028,-0.150798,-0.479985,0.183413,0.274296,-0.324834,-0.007945 EXPECTATIONS3=0.091780,-0.063723,-0.047316 VARIANCES0=0.178101,0.098278,0.133588,0.032554,0.174175,0.098719,0.099510,0.085478,0.125188,0.027032,0.024441,0.072028,0.030353,0.025179,0.055317,0.128881,0.041377,0.064303,0.084223,0.055170,0.132008,0.140905,0.068845,0.049277,0.122043,0.115459,0.032560,0.092613,0.189458,0.133222,0.157018,0.140573,0.069037,0.057995,0.129066,0.061241,0.053101,0.049235,0.033039,0.029835,0.094767,0.068893,0.058234,0.040725,0.177716,0.040645,0.017302,0.135656,0.176747,0.128018,0.082021,0.149770,0.171436,0.049722,0.082928,0.065581,0.092427,0.076881,0.098237,0.129117,0.058918,0.103728,0.103163,0.083126 VARIANCES1=0.706220,0.605285,0.554555,0.524657,0.594095,0.646251,0.621354,0.419902,0.509026,0.689563,0.500776,0.700943,0.708022,0.747216,0.573260,0.633179,0.530432,0.656365,0.682197,0.781312,0.716810,0.746948,0.695021,0.671969,0.589155,0.770663,0.693968,0.717936,0.729907,0.469842,0.616085,0.466044 VARIANCES2=0.603252,0.540821,0.362633,0.509901,0.573026,0.557948,0.514301,0.424526,0.687160,0.548119,0.595696,0.434592,0.471568,0.441397,0.460265,0.384788 VARIANCES3=0.371706,0.338737,0.345968 APPLY_BATCH_NORM ... ANNB
PBMETAD
Used to performed Parallel Bias metadynamics. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=ann.node-0,ann.node-1,ann.node-2
SIGMA
the widths of the Gaussian hills
=0.1,0.1,0.1
HEIGHT
the height of the Gaussian hills, one for all biases
=1.2
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
PACE
the frequency for hill addition, one for all biases
=500
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=5
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pb
FILE
files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found
=hills_pc0.out,hills_pc1.out,hills_pc2.out
GRID_MIN
the lower bounds for the grid
=-2.5,-2.5,-2.5
GRID_MAX
the upper bounds for the grid
=2.5,2.5,2.5
GRID_BIN
the number of bins for the grid
=5000,5000,5000 ... PBMETAD
# monitor the cv and the metadynamics bias potential
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=1
ARG
the input for this action is the scalar output from one or more other actions
=ann.node-0,ann.node-1,ann.node-2,pb.bias
FILE
the name of the file on which to output these quantities
=colvar.out