PLUMED-NEST

Project ID: plumID:24.014
Source: simulations/enhanced/plumed_files/plumed_TDA.dat
Originally used with PLUMED version: 2.9
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

# C-alpha contacts
cont1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=26 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont1 calculates the following quantities:
 Quantity   
 Description  
cont1.value
the value of the coordinationcont2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=47 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont2 calculates the following quantities:
 Quantity   
 Description  
cont2.value
the value of the coordinationcont3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=61 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont3 calculates the following quantities:
 Quantity   
 Description  
cont3.value
the value of the coordinationcont4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont4 calculates the following quantities:
 Quantity   
 Description  
cont4.value
the value of the coordinationcont5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont5 calculates the following quantities:
 Quantity   
 Description  
cont5.value
the value of the coordinationcont6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont6 calculates the following quantities:
 Quantity   
 Description  
cont6.value
the value of the coordinationcont7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont7 calculates the following quantities:
 Quantity   
 Description  
cont7.value
the value of the coordinationcont8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont8 calculates the following quantities:
 Quantity   
 Description  
cont8.value
the value of the coordinationcont9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont9 calculates the following quantities:
 Quantity   
 Description  
cont9.value
the value of the coordinationcont10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=47 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont10 calculates the following quantities:
 Quantity   
 Description  
cont10.value
the value of the coordinationcont11: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=61 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont11 calculates the following quantities:
 Quantity   
 Description  
cont11.value
the value of the coordinationcont12: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont12 calculates the following quantities:
 Quantity   
 Description  
cont12.value
the value of the coordinationcont13: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont13 calculates the following quantities:
 Quantity   
 Description  
cont13.value
the value of the coordinationcont14: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont14 calculates the following quantities:
 Quantity   
 Description  
cont14.value
the value of the coordinationcont15: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont15 calculates the following quantities:
 Quantity   
 Description  
cont15.value
the value of the coordinationcont16: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont16 calculates the following quantities:
 Quantity   
 Description  
cont16.value
the value of the coordinationcont17: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=26 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont17 calculates the following quantities:
 Quantity   
 Description  
cont17.value
the value of the coordinationcont18: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=61 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont18 calculates the following quantities:
 Quantity   
 Description  
cont18.value
the value of the coordinationcont19: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont19 calculates the following quantities:
 Quantity   
 Description  
cont19.value
the value of the coordinationcont20: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont20 calculates the following quantities:
 Quantity   
 Description  
cont20.value
the value of the coordinationcont21: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont21 calculates the following quantities:
 Quantity   
 Description  
cont21.value
the value of the coordinationcont22: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont22 calculates the following quantities:
 Quantity   
 Description  
cont22.value
the value of the coordinationcont23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont23 calculates the following quantities:
 Quantity   
 Description  
cont23.value
the value of the coordinationcont24: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont24 calculates the following quantities:
 Quantity   
 Description  
cont24.value
the value of the coordinationcont25: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=73 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont25 calculates the following quantities:
 Quantity   
 Description  
cont25.value
the value of the coordinationcont26: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont26 calculates the following quantities:
 Quantity   
 Description  
cont26.value
the value of the coordinationcont27: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont27 calculates the following quantities:
 Quantity   
 Description  
cont27.value
the value of the coordinationcont28: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont28 calculates the following quantities:
 Quantity   
 Description  
cont28.value
the value of the coordinationcont29: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont29 calculates the following quantities:
 Quantity   
 Description  
cont29.value
the value of the coordinationcont30: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=61 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont30 calculates the following quantities:
 Quantity   
 Description  
cont30.value
the value of the coordinationcont31: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=88 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont31 calculates the following quantities:
 Quantity   
 Description  
cont31.value
the value of the coordinationcont32: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont32 calculates the following quantities:
 Quantity   
 Description  
cont32.value
the value of the coordinationcont33: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont33 calculates the following quantities:
 Quantity   
 Description  
cont33.value
the value of the coordinationcont34: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont34 calculates the following quantities:
 Quantity   
 Description  
cont34.value
the value of the coordinationcont35: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=73 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont35 calculates the following quantities:
 Quantity   
 Description  
cont35.value
the value of the coordinationcont36: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=102 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont36 calculates the following quantities:
 Quantity   
 Description  
cont36.value
the value of the coordinationcont37: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont37 calculates the following quantities:
 Quantity   
 Description  
cont37.value
the value of the coordinationcont38: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont38 calculates the following quantities:
 Quantity   
 Description  
cont38.value
the value of the coordinationcont39: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=88 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont39 calculates the following quantities:
 Quantity   
 Description  
cont39.value
the value of the coordinationcont40: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=102 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=109 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont40 calculates the following quantities:
 Quantity   
 Description  
cont40.value
the value of the coordinationcont41: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=102 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont41 calculates the following quantities:
 Quantity   
 Description  
cont41.value
the value of the coordinationcont42: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=102 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont42 calculates the following quantities:
 Quantity   
 Description  
cont42.value
the value of the coordinationcont43: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=109 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=123 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont43 calculates the following quantities:
 Quantity   
 Description  
cont43.value
the value of the coordinationcont44: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=109 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}
The COORDINATION action with label cont44 calculates the following quantities:
 Quantity   
 Description  
cont44.value
the value of the coordinationcont45: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=123 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=147 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=6 MM=12}

# Neural network CV
The COORDINATION action with label cont45 calculates the following quantities:
 Quantity   
 Description  
cont45.value
the value of the coordinationdeep: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details ...
    FILEFilename of the PyTorch compiled model=TDA.pt
    ARGthe labels of the values from which the function is calculated=cont1,cont2,cont3,cont4,cont5,cont6,cont7,cont8,cont9,cont10,cont11,cont12,cont13,cont14,cont15,cont16,cont17,cont18,cont19,cont20,cont21,cont22,cont23,cont24,cont25,cont26,cont27,cont28,cont29,cont30,cont31,cont32,cont33,cont34,cont35,cont36,cont37,cont38,cont39,cont40,cont41,cont42,cont43,cont44,cont45
...

# Bias (WTM-eABF)
The PYTORCH_MODEL action with label deep calculates the following quantities:
 Quantity   
 Description  
deep.node
Model outputseabf: DRRUsed to performed extended-system adaptive biasing force (eABF) More details ...
    ARGthe labels of the scalars on which the bias will act=deep.node-0
    FULLSAMPLES number of samples in a bin prior to application of the ABF=500
    FRICTION add a friction to the variable, similar to extended Langevin Damping in Colvars=1.0
    TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=10
    TEMPthe system temperature - needed when FRICTION is present=340
    GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=-8.0
    GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=8.0
    GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1
    OUTPUTFREQwrite results to a file every N steps=10000000
...
The DRR action with label eabf calculates the following quantities:
 Quantity   
 Description  
eabf.bias
the instantaneous value of the bias potential
eabf._fict
one or multiple instances of this quantity can be referenced elsewhere in the input file
eabf._vfict
one or multiple instances of this quantity can be referenced elsewhere in the input file
eabf._biasforce
The bias force from eABF/DRR of the fictitious particle
eabf._springforce
Spring force between real CVs and extended CVs
eabf._fictNoPBC
the positions of fictitious particles (without PBC)wtmeabf: METADUsed to performed metadynamics on one or more collective variables. More details ...
    ARGthe labels of the scalars on which the bias will act=eabf.deep.node-0_fict
    PACEthe frequency for hill addition=500
    SIGMAthe widths of the Gaussian hills=0.2
    HEIGHTthe heights of the Gaussian hills=0.965
    TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=340
    BIASFACTORuse well tempered metadynamics and use this bias factor=12.765  # 4000 K
    GRID_MINthe lower bounds for the grid=-8.5
    GRID_MAXthe upper bounds for the grid=8.5
...

# Restraints
The METAD action with label wtmeabf calculates the following quantities:
 Quantity   
 Description  
wtmeabf.bias
the instantaneous value of the bias potentiallwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=eabf.deep.node-0_fict ATthe positions of the wall=-8.0 KAPPAthe force constant for the wall=100000
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=eabf.deep.node-0_fict ATthe positions of the wall=8.0 KAPPAthe force constant for the wall=100000

# Print
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1000 ARGthe labels of the values that you would like to print to the file=deep.node-0,eabf.deep.node-0_fict,lwall.bias,uwall.bias FILEthe name of the file on which to output these quantities=COLVAR
The PRINT action with label  calculates somethingFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=10000