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
tested onv2.10
tested onmaster
# 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}
cont2: 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}
cont3: 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}
cont4: 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}
cont5: 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}
cont6: 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}
cont7: 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}
cont8: 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}
cont9: 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}
cont10: 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}
cont11: 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}
cont12: 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}
cont13: 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}
cont14: 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}
cont15: 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}
cont16: 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}
cont17: 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}
cont18: 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}
cont19: 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}
cont20: 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}
cont21: 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}
cont22: 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}
cont23: 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}
cont24: 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}
cont25: 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}
cont26: 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}
cont27: 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}
cont28: 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}
cont29: 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}
cont30: 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}
cont31: 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}
cont32: 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}
cont33: 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}
cont34: 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}
cont35: 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}
cont36: 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}
cont37: 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}
cont38: 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}
cont39: 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}
cont40: 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}
cont41: 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}
cont42: 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}
cont43: 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}
cont44: 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}
cont45: 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
deep: 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)
eabf: DRRUsed to performed extended-system adaptive biasing force(eABF) This action has hidden defaults. 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
...
wtmeabf: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. 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
lwall: 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
uwall: 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
PRINTPrint 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
FLUSHThis 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