plumed_parameterized.dat

LOAD FILE=../../../src/pines/PINES.cpp
LOAD FILE=../../../src/annfunc/ANNB.cpp

PINES ...
LABEL=pines
PRECISION=10000
NLIST
ONLYDIRECT
REF_FILE=md.pdb
PINESATOMS=1
ATOMTYPES=Ar
SFACTOR=1.0
SORT=1.0
SWITCH1={RATIONAL R_0=0.56 MM=10 NN=5}
NL_CUTOFF=4.0
NL_STRIDE=1.0
NL_SKIN=0.1
... PINES

ANNB ...
LABEL=ann
ARG=pines.*
NUM_LAYERS=6
NUM_NODES=78,64,32,16,3,3
ACTIVATIONS=BNTanh,BNTanh,BNTanh,BNTanh,Linear
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WEIGHTS4=0.675073,-0.5784549,0.4578935,-0.7224135,-0.6442058,0.25123274,-0.14965081,0.5003888,0.85276955
BIASES0=-0.048063,0.098281,-0.090117,-0.166371,0.117707,-0.280313,-0.117921,-0.039746,-0.196697,0.265768,-0.183567,-0.195907,-0.108014,0.015663,-0.175535,0.223938,0.232270,0.204847,-0.403893,0.235392,0.012710,0.141278,-0.374090,0.048110,-0.148807,0.006374,-0.155035,0.137066,-0.335873,-0.419713,-0.083216,-0.097242,-0.100665,0.518453,0.543431,0.018895,0.142108,-0.120947,-0.122732,-0.447746,0.152872,-0.105704,-0.173332,0.069811,-0.004678,0.086060,-0.319264,0.132793,-0.099054,-0.140437,0.165657,0.120977,-0.354125,-0.208990,-0.137377,0.123939,0.090053,-0.229036,0.420433,-0.152860,-0.098012,-0.022714,0.338469,-0.017572
BIASES1=0.036732,0.348677,0.098118,0.105229,0.005452,-0.075277,-0.269871,-0.348018,0.039289,0.036608,-0.431258,-0.469405,0.356471,-0.006491,0.256913,-0.456220,-0.139893,0.185651,-0.258028,-0.056323,-0.021881,0.097827,-0.054179,-0.152560,-0.134301,-0.162530,-0.154957,-0.075378,-0.060240,0.040716,-0.203515,0.121625
BIASES2=-0.143864,-0.008947,-0.160072,0.093272,-0.003757,-0.194601,0.055391,-0.396276,0.093861,-0.137040,-0.155009,0.145065,-0.172337,-0.257718,-0.019015,-0.097332
BIASES3=-0.038223,0.031542,0.109945
BIASES4=0.0,0.0,0.0
GAMMAS0=0.917870,0.848360,0.911965,0.989852,0.898502,0.994605,0.954692,0.880492,0.905834,0.875644,0.835626,1.040972,0.886360,0.961458,0.922894,0.919989,0.981182,0.896130,0.976434,0.919483,0.896579,1.005141,1.021458,0.963003,0.952970,0.936634,0.975970,0.922005,0.968293,0.959213,0.930068,0.822378,0.924386,1.058211,1.043814,1.040816,0.878751,0.981764,0.993289,0.966895,0.980283,0.913147,0.887489,0.913462,0.949787,0.934356,0.926550,0.885000,0.923724,0.913635,0.845208,0.908723,0.907216,0.911296,0.851466,0.908542,0.921701,0.964888,0.974435,0.957270,0.946131,0.865645,0.902083,0.901463
GAMMAS1=0.966316,0.944616,0.906109,0.897219,0.944500,0.939601,0.916552,0.985350,0.937281,0.868850,0.961535,0.968672,0.948141,0.949862,0.890146,0.982906,0.941146,0.925267,0.977679,0.951762,0.936754,0.916383,0.936865,0.961362,0.975205,0.979632,0.935487,1.007427,0.931558,0.910312,0.903896,0.920016
GAMMAS2=0.977132,0.852315,0.995268,0.917420,0.969572,0.917869,0.837952,0.984380,0.949379,0.976679,0.951854,0.928722,0.940386,0.942385,0.935911,0.932981
GAMMAS3=0.982063,0.972953,0.960084
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BETAS1=0.091151,0.079927,-0.078951,0.162283,-0.050437,0.124352,-0.159730,0.036899,0.009705,-0.039096,-0.165098,-0.114566,0.162247,-0.135674,-0.113954,0.072985,-0.071864,-0.002605,-0.057134,0.190784,0.040376,0.059718,-0.015430,0.057172,0.128385,0.084040,-0.097043,0.049730,-0.119167,0.128232,0.030827,0.018322
BETAS2=0.099563,-0.019654,-0.096375,-0.073345,-0.089870,-0.100095,0.097684,0.097598,-0.022661,-0.005952,0.084413,0.068390,0.074848,0.073311,0.032562,-0.042645
BETAS3=-0.000472,-0.000583,0.002525
EXPECTATIONS0=0.691599,-0.554904,-0.772953,-0.838063,-0.835304,-0.676419,-0.958514,0.734097,0.166366,0.993500,-0.758141,-0.696519,-0.344244,0.871186,0.591530,-0.887980,0.867899,-0.414088,-0.290452,0.320429,0.731583,-0.155234,-0.955601,0.905945,-0.114175,-0.508952,0.049878,-0.197013,-0.826341,-0.580132,-0.917616,-0.112270,0.396548,0.884609,0.823846,0.820715,-0.468445,-0.848932,-0.066508,-0.639729,0.802994,0.362027,0.758625,0.973782,-0.997582,-0.904364,-0.014334,0.848622,-0.960600,-0.681344,0.523359,-0.696388,-0.767816,-0.921555,-0.793945,0.282530,0.622050,-0.967293,0.138608,-0.956447,0.367124,-0.449281,0.724482,0.693173
EXPECTATIONS1=-0.256114,0.776305,0.229058,0.077708,-0.033111,-0.077260,-0.756713,-0.670337,0.256687,0.295497,-0.750984,-0.722278,0.526809,0.234384,0.650865,-0.702436,-0.103027,0.395316,-0.515712,0.265192,-0.058550,0.052622,0.069930,-0.038229,-0.500864,-0.244020,-0.389433,-0.197949,0.035276,0.065562,-0.135684,0.095808
EXPECTATIONS2=-0.171919,-0.081447,-0.132188,0.077212,0.020611,-0.166674,0.069280,-0.369311,-0.064494,-0.108811,-0.009022,0.220215,-0.307543,-0.311112,0.036842,-0.143504
EXPECTATIONS3=0.020353,-0.005554,0.010257
VARIANCES0=0.086736,0.112788,0.108796,0.115179,0.086525,0.056407,0.039785,0.094451,0.114668,0.003944,0.122136,0.034428,0.124883,0.058170,0.069780,0.026862,0.019521,0.124861,0.118071,0.238412,0.142624,0.061361,0.024012,0.038847,0.062196,0.060633,0.151305,0.194038,0.042971,0.126289,0.053423,0.147590,0.143052,0.025593,0.139336,0.230786,0.084814,0.115553,0.047132,0.223954,0.019905,0.170266,0.072851,0.056752,0.005346,0.032434,0.080557,0.078577,0.031520,0.083263,0.126117,0.073282,0.124509,0.034198,0.085920,0.158251,0.054770,0.065905,0.135115,0.054835,0.093789,0.168395,0.086549,0.056556
VARIANCES1=0.673586,0.357590,0.390623,0.583279,0.799415,0.754594,0.251028,0.402803,0.671623,0.508880,0.309187,0.420236,0.364858,0.703167,0.282127,0.333251,0.748033,0.486752,0.533199,0.596983,0.629932,0.861961,0.780188,0.734383,0.437634,0.547159,0.547008,0.458779,0.717682,0.706740,0.643393,0.667163
VARIANCES2=0.480165,0.677401,0.677029,0.637025,0.575540,0.398277,0.401198,0.486252,0.632345,0.372918,0.839733,0.409889,0.382777,0.291593,0.776022,0.393293
VARIANCES3=0.328479,0.356984,0.353548
APPLY_BATCH_NORM
... ANNB


PBMETAD ...
ARG=ann.node-0,ann.node-1,ann.node-2 SIGMA=0.1,0.1,0.1 HEIGHT=0.25
TEMP=50 PACE=500 BIASFACTOR=2 LABEL=pb
FILE=hills_pc0.out,hills_pc1.out,hills_pc2.out
GRID_MIN=-2.5,-2.5,-2.5 GRID_MAX=2.5,2.5,2.5 GRID_BIN=5000,5000,5000
... PBMETAD

# monitor the cv and the metadynamics bias potential
PRINT STRIDE=1 ARG=ann.node-0,ann.node-1,ann.node-2,pb.bias FILE=colvar.out