PLUMED-NEST

Project ID: plumID:23.024
Source: examples/driverTests/plumed_NaCl.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

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=../../src/pines/PINES.cpp
The LOAD action with label  calculates something
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/NaCl/md.pdb
PINESATOMS=5
ATOMTYPES=NA,CL,OW,HW1,HW2
SFACTOR=1.0,1.0,1.0,1.0,1.0
SORT=1.0,1.0,1.0,1.0,1.0
SWITCH1={RATIONAL R_0=0.38 MM=12 NN=6}
SWITCH2={RATIONAL R_0=0.35 MM=12 NN=6}
SWITCH3={RATIONAL R_0=0.41 MM=12 NN=6}
SWITCH4={RATIONAL R_0=0.40 MM=12 NN=6}
SWITCH5={RATIONAL R_0=0.28 MM=12 NN=6}
NL_CUTOFF=5.0,1.5,1.5,1.5,1.5
NL_STRIDE=10.0,10.0,10.0,10.0,10.0
NL_SKIN=0.1,0.1,0.1,0.1,0.1
NL_CONSTANT_SIZE=10
... 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=61,64,32,16,3,3
ACTIVATIONS=BNTanh,BNTanh,BNTanh,BNTanh,Linear
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WEIGHTS4=-0.6394422,-0.37072414,-0.67355573,0.6776882,-0.6855342,-0.26604843,-0.36311483,-0.6265835,0.68959486
BIASES0=0.060985,0.032023,-0.051266,-0.028931,-0.015705,-0.145292,-0.076389,-0.095456,-0.031824,0.167867,-0.129107,0.080049,0.041918,0.048593,0.066266,0.070097,0.118467,0.120353,-0.139361,-0.092079,0.171404,0.019148,-0.066094,0.036726,0.044208,0.152737,0.088558,-0.055361,0.129396,0.087279,-0.144771,0.150891,-0.067743,-0.124376,0.111282,-0.063581,0.160143,0.033849,-0.031837,-0.030054,0.049182,0.035730,0.034751,0.036564,0.011086,0.009447,-0.073366,-0.053866,0.042857,0.059736,-0.085095,-0.122617,0.010960,-0.058719,0.099811,-0.059642,-0.081215,-0.014468,-0.076659,-0.023982,-0.203126,-0.059731,-0.064434,-0.122612
BIASES1=0.071895,-0.102403,-0.008515,-0.065381,-0.063475,0.001546,0.137189,0.133912,0.224891,-0.043075,-0.021972,0.161509,-0.010783,0.085254,0.070937,-0.006965,-0.029957,0.062829,-0.081809,0.106723,-0.262453,0.144735,-0.154858,0.168913,0.095719,-0.083627,0.005792,-0.078513,0.090871,0.091231,0.102217,-0.153369
BIASES2=0.190462,0.032838,-0.095164,-0.210477,0.072552,-0.243745,0.143753,0.056373,0.154957,-0.014666,-0.132158,-0.120612,0.265325,-0.013559,-0.144497,-0.119660
BIASES3=-0.185973,0.079348,0.069783
BIASES4=0.0,0.0,0.0
GAMMAS0=1.003171,0.967903,0.992257,0.990191,0.996550,1.002286,0.992314,0.991374,0.957796,0.977995,1.015435,0.980501,1.000442,0.984067,0.969332,0.992316,0.960547,0.991223,0.985661,1.005276,0.990929,0.997547,1.000376,0.990051,0.993697,1.045823,0.965338,0.994325,0.994375,0.981484,0.993908,0.953013,0.960373,1.006256,0.985232,0.974083,0.990764,1.008798,0.995703,0.976286,0.991421,0.994270,0.991440,0.991988,0.985096,1.004411,1.013048,0.983834,0.955501,0.967920,0.988435,0.957506,1.003416,0.936211,1.023164,0.985219,0.968761,0.965332,1.006228,0.977901,1.024104,0.947266,0.934591,0.998376
GAMMAS1=0.974856,0.960320,0.981271,0.977489,1.011168,0.984357,0.996363,1.003064,1.000832,0.998383,0.993558,0.993375,0.961865,0.968394,1.016550,1.019333,0.997143,0.968139,0.996138,0.994429,1.023538,0.982449,1.005742,0.961460,0.966869,0.973451,0.979368,1.003142,0.991272,0.985678,0.978619,1.006234
GAMMAS2=0.983697,0.985202,0.964772,0.971414,0.980088,0.965015,0.977825,0.998382,0.984879,0.964914,0.980601,0.983862,1.004825,0.987470,0.996967,0.992458
GAMMAS3=0.970631,0.960477,0.959502
BETAS0=-0.138535,-0.086551,-0.024183,0.039940,-0.020175,0.066877,0.030727,0.006858,0.045242,-0.052161,-0.054055,0.046544,0.008220,0.123127,0.044338,-0.113864,0.052599,0.030287,0.001288,-0.047925,0.059126,-0.118080,-0.062531,0.028628,0.148444,0.164645,-0.004282,0.004639,0.033558,-0.048763,0.065518,-0.044138,-0.003033,0.099663,-0.030382,-0.109728,-0.017186,0.049327,-0.065815,-0.016627,-0.037357,0.245023,-0.010361,-0.012299,0.001012,0.097104,0.040221,0.060521,-0.036354,0.007759,-0.041999,0.051344,0.030035,0.014287,0.029464,-0.130576,-0.052002,-0.070714,-0.017912,0.038522,-0.052772,-0.042579,0.117716,0.003067
BETAS1=-0.098673,0.073261,0.043575,0.063541,-0.042749,0.043838,0.050393,0.047642,0.091244,0.104698,0.066408,0.038135,-0.037138,0.011378,-0.035607,-0.167248,0.127696,-0.032705,0.017790,-0.069741,-0.050211,0.002165,-0.070437,0.069386,0.055810,0.118255,0.051102,-0.097057,0.046259,0.079029,0.093027,0.056679
BETAS2=0.053291,-0.038681,0.043515,0.055156,0.037211,-0.014494,-0.020963,0.036870,0.018773,-0.006060,0.017509,0.029301,0.022549,0.031406,0.009085,0.003973
BETAS3=0.001281,-0.005440,-0.002466
EXPECTATIONS0=-0.415922,-0.593043,0.175686,-0.396270,0.239863,-0.262788,-0.258499,-0.928662,0.440009,0.768921,0.186050,-0.361677,0.389950,0.189968,-0.498567,0.415350,0.027727,0.904694,-0.614407,-0.290966,0.833690,-0.088038,-0.368264,0.261534,-0.002266,0.134915,-0.203360,-0.055174,0.727800,-0.107577,-0.943987,0.442505,0.636094,-0.101334,0.690116,-0.213983,0.778901,0.747579,-0.580126,0.642011,0.075632,-0.168538,0.323087,0.133097,0.875053,0.149805,-0.074911,-0.203589,-0.686323,0.028714,-0.373533,-0.389814,-0.028611,-0.973631,0.232735,0.026090,0.810998,0.572804,0.360141,0.112596,-0.409714,-0.276223,0.599141,-0.629471
EXPECTATIONS1=-0.009037,-0.088459,0.017084,-0.086998,-0.093062,-0.108064,0.025702,0.187932,0.225901,-0.046820,0.032285,0.236120,-0.039862,0.037627,0.028076,-0.043647,-0.027451,0.023103,-0.097207,0.048663,-0.295987,0.112813,-0.217827,0.158566,0.027806,-0.070303,0.045887,-0.099764,0.013873,0.030691,0.051859,-0.249066
EXPECTATIONS2=0.200793,0.033372,-0.073594,-0.175195,0.100994,-0.280713,0.092933,0.065659,0.032260,-0.077834,-0.054368,-0.131239,0.300242,-0.019541,-0.051866,-0.080708
EXPECTATIONS3=-0.115060,0.037335,0.031417
VARIANCES0=0.052240,0.034196,0.058380,0.055721,0.061063,0.048904,0.035384,0.012330,0.057826,0.034547,0.065619,0.038724,0.044961,0.037138,0.040491,0.042173,0.044672,0.017191,0.041901,0.050601,0.025177,0.052597,0.045743,0.058819,0.045317,0.047096,0.047028,0.037104,0.026922,0.048272,0.010833,0.041805,0.030412,0.061888,0.040588,0.047167,0.028473,0.037889,0.035710,0.035066,0.061532,0.056918,0.052560,0.054027,0.021990,0.047943,0.046269,0.038681,0.030963,0.048141,0.049016,0.041114,0.062320,0.004812,0.043127,0.038738,0.025947,0.041527,0.053211,0.038037,0.035779,0.039128,0.030128,0.055516
VARIANCES1=0.571717,0.633636,0.509191,0.541526,0.507304,0.550888,0.684315,0.421193,0.504235,0.555232,0.590806,0.554174,0.402739,0.702549,0.505615,0.411226,0.445298,0.493958,0.624664,0.511030,0.546815,0.404176,0.546112,0.472236,0.491740,0.593674,0.522206,0.675024,0.648990,0.778235,0.585932,0.603458
VARIANCES2=0.538119,0.428904,0.478671,0.547601,0.487733,0.495726,0.517372,0.577776,0.635278,0.537352,0.569003,0.408329,0.495555,0.598601,0.680160,0.597270
VARIANCES3=0.368145,0.393454,0.424648
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
=2 
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_pc2.out,hills_pc3.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
The PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Description  
pb.bias
the instantaneous value of the 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