PLUMED-NEST by plumed-nest

Project ID: plumID:19.083
Source: Reaction_discovery/1.H2_NO/plumed.dat
Originally used with PLUMED version: 2.5
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
RESTARTActivate restart. More details
The RESTART action with label  calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

NThe GROUP action with label N calculates the following quantities: Quantity    Type    Description  
N atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1,3
OThe GROUP action with label O calculates the following quantities: Quantity    Type    Description  
O atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2,4
HThe GROUP action with label H calculates the following quantities: Quantity    Type    Description  
H atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5,6,7,8

hhThe COORDINATIONNUMBER action with label hh calculates the following quantities: Quantity    Type    Description  
hh vector the coordination numbers of the specified atoms
hh_mean scalar the mean of the colvars: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=H SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# hh: COORDINATIONNUMBER SPECIES=H SWITCH={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8} MEAN
# as follows (Click the red comment above to revert to the short version of the input):
hh_grpThe GROUP action with label hh_grp calculates the following quantities: Quantity    Type    Description  
hh_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=H
hh_matThe CONTACT_MATRIX action with label hh_mat calculates the following quantities: Quantity    Type    Description  
hh_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=H SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.1 NN=6 MM=8}
hh_onesThe CONSTANT action with label hh_ones calculates the following quantities: Quantity    Type    Description  
hh_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=4
hhThe MATRIX_VECTOR_PRODUCT action with label hh calculates the following quantities: Quantity    Type    Description  
hh vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=hh_mat,hh_ones
hh_caverageThe MEAN action with label hh_caverage calculates the following quantities: Quantity    Type    Description  
hh_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=hh PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hh_meanThe MEAN action with label hh_mean calculates the following quantities: Quantity    Type    Description  
hh_mean scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=hh PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- nnThe COORDINATIONNUMBER action with label nn calculates the following quantities: Quantity    Type    Description  
nn vector the coordination numbers of the specified atoms
nn_mean scalar the mean of the colvars: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=N SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.5 NN=6 MM=8} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# nn: COORDINATIONNUMBER SPECIES=N SWITCH={RATIONAL D_0=0.0 R_0=1.5 NN=6 MM=8} MEAN
# as follows (Click the red comment above to revert to the short version of the input):
nn_grpThe GROUP action with label nn_grp calculates the following quantities: Quantity    Type    Description  
nn_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=N
nn_matThe CONTACT_MATRIX action with label nn_mat calculates the following quantities: Quantity    Type    Description  
nn_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=N SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.5 NN=6 MM=8}
nn_onesThe CONSTANT action with label nn_ones calculates the following quantities: Quantity    Type    Description  
nn_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=2
nnThe MATRIX_VECTOR_PRODUCT action with label nn calculates the following quantities: Quantity    Type    Description  
nn vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=nn_mat,nn_ones
nn_caverageThe MEAN action with label nn_caverage calculates the following quantities: Quantity    Type    Description  
nn_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=nn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nn_meanThe MEAN action with label nn_mean calculates the following quantities: Quantity    Type    Description  
nn_mean scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=nn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ooThe COORDINATIONNUMBER action with label oo calculates the following quantities: Quantity    Type    Description  
oo vector the coordination numbers of the specified atoms
oo_mean scalar the mean of the colvars: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=O SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# oo: COORDINATIONNUMBER SPECIES=O SWITCH={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8} MEAN
# as follows (Click the red comment above to revert to the short version of the input):
oo_grpThe GROUP action with label oo_grp calculates the following quantities: Quantity    Type    Description  
oo_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=O
oo_matThe CONTACT_MATRIX action with label oo_mat calculates the following quantities: Quantity    Type    Description  
oo_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=O SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.7 NN=6 MM=8}
oo_onesThe CONSTANT action with label oo_ones calculates the following quantities: Quantity    Type    Description  
oo_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=2
ooThe MATRIX_VECTOR_PRODUCT action with label oo calculates the following quantities: Quantity    Type    Description  
oo vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=oo_mat,oo_ones
oo_caverageThe MEAN action with label oo_caverage calculates the following quantities: Quantity    Type    Description  
oo_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=oo PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
oo_meanThe MEAN action with label oo_mean calculates the following quantities: Quantity    Type    Description  
oo_mean scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=oo PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- noThe COORDINATIONNUMBER action with label no calculates the following quantities: Quantity    Type    Description  
no vector the coordination numbers of the specified atoms
no_min scalar the minimum colvar
no_max scalar the maximum colvar: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=O SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# no: COORDINATIONNUMBER SPECIESA=N SPECIESB=O SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} MIN={BETA=20.0} MAX={BETA=0.02}
# as follows (Click the red comment above to revert to the short version of the input):
no_grpThe GROUP action with label no_grp calculates the following quantities: Quantity    Type    Description  
no_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=N
no_matThe CONTACT_MATRIX action with label no_mat calculates the following quantities: Quantity    Type    Description  
no_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=N GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=O SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
no_onesThe CONSTANT action with label no_ones calculates the following quantities: Quantity    Type    Description  
no_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=2
noThe MATRIX_VECTOR_PRODUCT action with label no calculates the following quantities: Quantity    Type    Description  
no vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=no_mat,no_ones
no_caverageThe MEAN action with label no_caverage calculates the following quantities: Quantity    Type    Description  
no_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=no PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
no_me_minThe CUSTOM action with label no_me_min calculates the following quantities: Quantity    Type    Description  
no_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=no FUNCthe function you wish to evaluate=exp(20.0/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
no_mec_minThe SUM action with label no_mec_min calculates the following quantities: Quantity    Type    Description  
no_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=no_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
no_minThe CUSTOM action with label no_min calculates the following quantities: Quantity    Type    Description  
no_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=no_mec_min FUNCthe function you wish to evaluate=20.0/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
no_me_maxThe CUSTOM action with label no_me_max calculates the following quantities: Quantity    Type    Description  
no_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=no FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
no_mec_maxThe SUM action with label no_mec_max calculates the following quantities: Quantity    Type    Description  
no_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=no_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
no_maxThe CUSTOM action with label no_max calculates the following quantities: Quantity    Type    Description  
no_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=no_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- onThe COORDINATIONNUMBER action with label on calculates the following quantities: Quantity    Type    Description  
on vector the coordination numbers of the specified atoms
on_min scalar the minimum colvar
on_max scalar the maximum colvar: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=O SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=N SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# on: COORDINATIONNUMBER SPECIESA=O SPECIESB=N SWITCH={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8} MIN={BETA=20.0} MAX={BETA=0.02}
# as follows (Click the red comment above to revert to the short version of the input):
on_grpThe GROUP action with label on_grp calculates the following quantities: Quantity    Type    Description  
on_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=O
on_matThe CONTACT_MATRIX action with label on_mat calculates the following quantities: Quantity    Type    Description  
on_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=O GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=N SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.6 NN=6 MM=8}
on_onesThe CONSTANT action with label on_ones calculates the following quantities: Quantity    Type    Description  
on_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=2
onThe MATRIX_VECTOR_PRODUCT action with label on calculates the following quantities: Quantity    Type    Description  
on vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=on_mat,on_ones
on_caverageThe MEAN action with label on_caverage calculates the following quantities: Quantity    Type    Description  
on_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=on PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
on_me_minThe CUSTOM action with label on_me_min calculates the following quantities: Quantity    Type    Description  
on_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=on FUNCthe function you wish to evaluate=exp(20.0/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
on_mec_minThe SUM action with label on_mec_min calculates the following quantities: Quantity    Type    Description  
on_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=on_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
on_minThe CUSTOM action with label on_min calculates the following quantities: Quantity    Type    Description  
on_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=on_mec_min FUNCthe function you wish to evaluate=20.0/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
on_me_maxThe CUSTOM action with label on_me_max calculates the following quantities: Quantity    Type    Description  
on_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=on FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
on_mec_maxThe SUM action with label on_mec_max calculates the following quantities: Quantity    Type    Description  
on_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=on_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
on_maxThe CUSTOM action with label on_max calculates the following quantities: Quantity    Type    Description  
on_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=on_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- nhThe COORDINATIONNUMBER action with label nh calculates the following quantities: Quantity    Type    Description  
nh vector the coordination numbers of the specified atoms
nh_min scalar the minimum colvar
nh_max scalar the maximum colvar: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=H SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# nh: COORDINATIONNUMBER SPECIESA=N SPECIESB=H SWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MIN={BETA=20.0} MAX={BETA=0.02}
# as follows (Click the red comment above to revert to the short version of the input):
nh_grpThe GROUP action with label nh_grp calculates the following quantities: Quantity    Type    Description  
nh_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=N
nh_matThe CONTACT_MATRIX action with label nh_mat calculates the following quantities: Quantity    Type    Description  
nh_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=N GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=H SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}
nh_onesThe CONSTANT action with label nh_ones calculates the following quantities: Quantity    Type    Description  
nh_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=4
nhThe MATRIX_VECTOR_PRODUCT action with label nh calculates the following quantities: Quantity    Type    Description  
nh vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=nh_mat,nh_ones
nh_caverageThe MEAN action with label nh_caverage calculates the following quantities: Quantity    Type    Description  
nh_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=nh PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nh_me_minThe CUSTOM action with label nh_me_min calculates the following quantities: Quantity    Type    Description  
nh_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=nh FUNCthe function you wish to evaluate=exp(20.0/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nh_mec_minThe SUM action with label nh_mec_min calculates the following quantities: Quantity    Type    Description  
nh_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=nh_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nh_minThe CUSTOM action with label nh_min calculates the following quantities: Quantity    Type    Description  
nh_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=nh_mec_min FUNCthe function you wish to evaluate=20.0/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nh_me_maxThe CUSTOM action with label nh_me_max calculates the following quantities: Quantity    Type    Description  
nh_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=nh FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nh_mec_maxThe SUM action with label nh_mec_max calculates the following quantities: Quantity    Type    Description  
nh_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=nh_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nh_maxThe CUSTOM action with label nh_max calculates the following quantities: Quantity    Type    Description  
nh_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=nh_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- hnThe COORDINATIONNUMBER action with label hn calculates the following quantities: Quantity    Type    Description  
hn vector the coordination numbers of the specified atoms
hn_min scalar the minimum colvar
hn_max scalar the maximum colvar: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=H SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=N SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# hn: COORDINATIONNUMBER SPECIESA=H SPECIESB=N SWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MIN={BETA=20.0} MAX={BETA=0.02}
# as follows (Click the red comment above to revert to the short version of the input):
hn_grpThe GROUP action with label hn_grp calculates the following quantities: Quantity    Type    Description  
hn_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=H
hn_matThe CONTACT_MATRIX action with label hn_mat calculates the following quantities: Quantity    Type    Description  
hn_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=H GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=N SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}
hn_onesThe CONSTANT action with label hn_ones calculates the following quantities: Quantity    Type    Description  
hn_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=2
hnThe MATRIX_VECTOR_PRODUCT action with label hn calculates the following quantities: Quantity    Type    Description  
hn vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=hn_mat,hn_ones
hn_caverageThe MEAN action with label hn_caverage calculates the following quantities: Quantity    Type    Description  
hn_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=hn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hn_me_minThe CUSTOM action with label hn_me_min calculates the following quantities: Quantity    Type    Description  
hn_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hn FUNCthe function you wish to evaluate=exp(20.0/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hn_mec_minThe SUM action with label hn_mec_min calculates the following quantities: Quantity    Type    Description  
hn_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=hn_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hn_minThe CUSTOM action with label hn_min calculates the following quantities: Quantity    Type    Description  
hn_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hn_mec_min FUNCthe function you wish to evaluate=20.0/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hn_me_maxThe CUSTOM action with label hn_me_max calculates the following quantities: Quantity    Type    Description  
hn_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hn FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hn_mec_maxThe SUM action with label hn_mec_max calculates the following quantities: Quantity    Type    Description  
hn_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=hn_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hn_maxThe CUSTOM action with label hn_max calculates the following quantities: Quantity    Type    Description  
hn_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hn_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ohThe COORDINATIONNUMBER action with label oh calculates the following quantities: Quantity    Type    Description  
oh vector the coordination numbers of the specified atoms
oh_min scalar the minimum colvar
oh_max scalar the maximum colvar: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=O SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=H SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# oh: COORDINATIONNUMBER SPECIESA=O SPECIESB=H SWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MIN={BETA=20.0} MAX={BETA=0.02}
# as follows (Click the red comment above to revert to the short version of the input):
oh_grpThe GROUP action with label oh_grp calculates the following quantities: Quantity    Type    Description  
oh_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=O
oh_matThe CONTACT_MATRIX action with label oh_mat calculates the following quantities: Quantity    Type    Description  
oh_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=O GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=H SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}
oh_onesThe CONSTANT action with label oh_ones calculates the following quantities: Quantity    Type    Description  
oh_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=4
ohThe MATRIX_VECTOR_PRODUCT action with label oh calculates the following quantities: Quantity    Type    Description  
oh vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=oh_mat,oh_ones
oh_caverageThe MEAN action with label oh_caverage calculates the following quantities: Quantity    Type    Description  
oh_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=oh PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
oh_me_minThe CUSTOM action with label oh_me_min calculates the following quantities: Quantity    Type    Description  
oh_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=oh FUNCthe function you wish to evaluate=exp(20.0/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
oh_mec_minThe SUM action with label oh_mec_min calculates the following quantities: Quantity    Type    Description  
oh_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=oh_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
oh_minThe CUSTOM action with label oh_min calculates the following quantities: Quantity    Type    Description  
oh_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=oh_mec_min FUNCthe function you wish to evaluate=20.0/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
oh_me_maxThe CUSTOM action with label oh_me_max calculates the following quantities: Quantity    Type    Description  
oh_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=oh FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
oh_mec_maxThe SUM action with label oh_mec_max calculates the following quantities: Quantity    Type    Description  
oh_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=oh_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
oh_maxThe CUSTOM action with label oh_max calculates the following quantities: Quantity    Type    Description  
oh_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=oh_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- hoThe COORDINATIONNUMBER action with label ho calculates the following quantities: Quantity    Type    Description  
ho vector the coordination numbers of the specified atoms
ho_min scalar the minimum colvar
ho_max scalar the maximum colvar: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=H SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=O SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# ho: COORDINATIONNUMBER SPECIESA=H SPECIESB=O SWITCH={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8} MIN={BETA=20.0} MAX={BETA=0.02}
# as follows (Click the red comment above to revert to the short version of the input):
ho_grpThe GROUP action with label ho_grp calculates the following quantities: Quantity    Type    Description  
ho_grp atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=H
ho_matThe CONTACT_MATRIX action with label ho_mat calculates the following quantities: Quantity    Type    Description  
ho_mat matrix a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=H GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=O SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=1.4 NN=6 MM=8}
ho_onesThe CONSTANT action with label ho_ones calculates the following quantities: Quantity    Type    Description  
ho_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=2
hoThe MATRIX_VECTOR_PRODUCT action with label ho calculates the following quantities: Quantity    Type    Description  
ho vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details  ARGthe label for the matrix and the vector/scalar that are being multiplied=ho_mat,ho_ones
ho_caverageThe MEAN action with label ho_caverage calculates the following quantities: Quantity    Type    Description  
ho_caverage scalar the mean of all the elements in the input vector: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=ho PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ho_me_minThe CUSTOM action with label ho_me_min calculates the following quantities: Quantity    Type    Description  
ho_me_min vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ho FUNCthe function you wish to evaluate=exp(20.0/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ho_mec_minThe SUM action with label ho_mec_min calculates the following quantities: Quantity    Type    Description  
ho_mec_min scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=ho_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ho_minThe CUSTOM action with label ho_min calculates the following quantities: Quantity    Type    Description  
ho_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ho_mec_min FUNCthe function you wish to evaluate=20.0/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ho_me_maxThe CUSTOM action with label ho_me_max calculates the following quantities: Quantity    Type    Description  
ho_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ho FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ho_mec_maxThe SUM action with label ho_mec_max calculates the following quantities: Quantity    Type    Description  
ho_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=ho_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ho_maxThe CUSTOM action with label ho_max calculates the following quantities: Quantity    Type    Description  
ho_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ho_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
d1The COMBINE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=hh.mean COEFFICIENTS the coefficients of the arguments in your function=1.00 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d2The COMBINE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=nn.mean COEFFICIENTS the coefficients of the arguments in your function=1.0734 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d3The COMBINE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=oo.mean COEFFICIENTS the coefficients of the arguments in your function=1.6782 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d4The COMBINE action with label d4 calculates the following quantities: Quantity    Type    Description  
d4 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=no.max COEFFICIENTS the coefficients of the arguments in your function=0.7097 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d5The COMBINE action with label d5 calculates the following quantities: Quantity    Type    Description  
d5 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=no.min COEFFICIENTS the coefficients of the arguments in your function=0.7637 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d6The COMBINE action with label d6 calculates the following quantities: Quantity    Type    Description  
d6 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=on.max COEFFICIENTS the coefficients of the arguments in your function=0.7121 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d7The COMBINE action with label d7 calculates the following quantities: Quantity    Type    Description  
d7 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=on.min COEFFICIENTS the coefficients of the arguments in your function=0.7643 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d8The COMBINE action with label d8 calculates the following quantities: Quantity    Type    Description  
d8 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=nh.max COEFFICIENTS the coefficients of the arguments in your function=0.9618 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d9The COMBINE action with label d9 calculates the following quantities: Quantity    Type    Description  
d9 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=nh.min COEFFICIENTS the coefficients of the arguments in your function=1.1010 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d10The COMBINE action with label d10 calculates the following quantities: Quantity    Type    Description  
d10 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=hn.max COEFFICIENTS the coefficients of the arguments in your function=1.3052 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d11The COMBINE action with label d11 calculates the following quantities: Quantity    Type    Description  
d11 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=hn.min COEFFICIENTS the coefficients of the arguments in your function=2.5949 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d12The COMBINE action with label d12 calculates the following quantities: Quantity    Type    Description  
d12 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=oh.max COEFFICIENTS the coefficients of the arguments in your function=0.3617 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d13The COMBINE action with label d13 calculates the following quantities: Quantity    Type    Description  
d13 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=oh.min COEFFICIENTS the coefficients of the arguments in your function=0.4227 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d14The COMBINE action with label d14 calculates the following quantities: Quantity    Type    Description  
d14 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ho.max COEFFICIENTS the coefficients of the arguments in your function=0.6276 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d15The COMBINE action with label d15 calculates the following quantities: Quantity    Type    Description  
d15 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ho.min COEFFICIENTS the coefficients of the arguments in your function=0.8866 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#the following are 32,33,34
svd14The COMBINE action with label svd14 calculates the following quantities: Quantity    Type    Description  
svd14 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15 COEFFICIENTS the coefficients of the arguments in your function=0.0,-0.02114,0.00334,-0.23391,-0.64088,0.21637,0.69767,0.00113,-0.00213,-0.00001,0.00025,0.00206,-0.00739,-0.00457,-0.02124 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
svd13The COMBINE action with label svd13 calculates the following quantities: Quantity    Type    Description  
svd13 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15 COEFFICIENTS the coefficients of the arguments in your function=0.0,-0.39547,0.06121,-0.20744,0.60671,-0.11341,0.47938,0.02201,-0.03897,-0.00129,0.00439,0.03726,-0.13914,-0.08409,-0.39524 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
svd12The COMBINE action with label svd12 calculates the following quantities: Quantity    Type    Description  
svd12 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15 COEFFICIENTS the coefficients of the arguments in your function=0.0,-0.40711,0.06514,-0.17925,0.61216,-0.15080,0.50432,0.02309,-0.04043,-0.00128,0.00438,-0.02035,-0.27076,-0.03965,-0.26189 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

dNNThe DISTANCES action with label dNN calculates the following quantities: Quantity    Type    Description  
dNN vector the DISTANCES between the each pair of atoms that were specified
dNN_max scalar the maximum colvar: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N MAXcalculate the maximum value={BETA=0.02} NOPBC ignore the periodic boundary conditions when calculating distances
# PLUMED interprets the command:
# dNN: DISTANCES GROUPA=N GROUPB=N MAX={BETA=0.02} NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
dNNThe DISTANCE action with label dNN calculates the following quantities: Quantity    Type    Description  
dNN vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the pair of atom that we are calculating the distance between=1,1 ATOMS2the pair of atom that we are calculating the distance between=1,3 ATOMS3the pair of atom that we are calculating the distance between=3,1 ATOMS4the pair of atom that we are calculating the distance between=3,3
dNN_me_maxThe CUSTOM action with label dNN_me_max calculates the following quantities: Quantity    Type    Description  
dNN_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNN FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNN_mec_maxThe SUM action with label dNN_mec_max calculates the following quantities: Quantity    Type    Description  
dNN_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=dNN_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNN_maxThe CUSTOM action with label dNN_max calculates the following quantities: Quantity    Type    Description  
dNN_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNN_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dNHThe DISTANCES action with label dNH calculates the following quantities: Quantity    Type    Description  
dNH vector the DISTANCES between the each pair of atoms that were specified
dNH_max scalar the maximum colvar: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MAXcalculate the maximum value={BETA=0.02} NOPBC ignore the periodic boundary conditions when calculating distances
# PLUMED interprets the command:
# dNH: DISTANCES GROUPA=N GROUPB=H MAX={BETA=0.02} NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
dNHThe DISTANCE action with label dNH calculates the following quantities: Quantity    Type    Description  
dNH vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the pair of atom that we are calculating the distance between=1,5 ATOMS2the pair of atom that we are calculating the distance between=1,6 ATOMS3the pair of atom that we are calculating the distance between=1,7 ATOMS4the pair of atom that we are calculating the distance between=1,8 ATOMS5the pair of atom that we are calculating the distance between=3,5     # Action input conctinues with 3 further ATOMSn keywords, 
dNH_me_maxThe CUSTOM action with label dNH_me_max calculates the following quantities: Quantity    Type    Description  
dNH_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNH FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNH_mec_maxThe SUM action with label dNH_mec_max calculates the following quantities: Quantity    Type    Description  
dNH_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=dNH_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNH_maxThe CUSTOM action with label dNH_max calculates the following quantities: Quantity    Type    Description  
dNH_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNH_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- dOOThe DISTANCES action with label dOO calculates the following quantities: Quantity    Type    Description  
dOO vector the DISTANCES between the each pair of atoms that were specified
dOO_max scalar the maximum colvar: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=O GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=O MAXcalculate the maximum value={BETA=0.02} NOPBC ignore the periodic boundary conditions when calculating distances
# PLUMED interprets the command:
# dOO: DISTANCES GROUPA=O GROUPB=O MAX={BETA=0.02} NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
dOOThe DISTANCE action with label dOO calculates the following quantities: Quantity    Type    Description  
dOO vector the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the pair of atom that we are calculating the distance between=2,2 ATOMS2the pair of atom that we are calculating the distance between=2,4 ATOMS3the pair of atom that we are calculating the distance between=4,2 ATOMS4the pair of atom that we are calculating the distance between=4,4
dOO_me_maxThe CUSTOM action with label dOO_me_max calculates the following quantities: Quantity    Type    Description  
dOO_me_max vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dOO FUNCthe function you wish to evaluate=exp(x/0.02) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dOO_mec_maxThe SUM action with label dOO_mec_max calculates the following quantities: Quantity    Type    Description  
dOO_mec_max scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=dOO_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dOO_maxThe CUSTOM action with label dOO_max calculates the following quantities: Quantity    Type    Description  
dOO_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dOO_mec_max FUNCthe function you wish to evaluate=0.02*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- wallNNThe UPPER_WALLS action with label wallNN calculates the following quantities: Quantity    Type    Description  
wallNN.bias scalar the instantaneous value of the bias potential
wallNN.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dNN.max ATthe positions of the wall=9.0 KAPPAthe force constant for the wall=200.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 
wallNHThe UPPER_WALLS action with label wallNH calculates the following quantities: Quantity    Type    Description  
wallNH.bias scalar the instantaneous value of the bias potential
wallNH.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dNH.max ATthe positions of the wall=9.0 KAPPAthe force constant for the wall=200.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1 
wallNaNThe UPPER_WALLS action with label wallNaN calculates the following quantities: Quantity    Type    Description  
wallNaN.bias scalar the instantaneous value of the bias potential
wallNaN.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dOO.max ATthe positions of the wall=9.0 KAPPAthe force constant for the wall=200.0 EXP the powers for the walls=2 EPS the values for s_i in the expression for a wall=1

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=svd13 SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=3.0 PACEthe frequency for hill addition=100 LABELa label for the action so that its output can be referenced in the input to other actions=restraintThe METAD action with label restraint calculates the following quantities: Quantity    Type    Description  
restraint.bias scalar the instantaneous value of the bias potential 
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
   ARGthe labels of the scalars on which the bias will act=svd13 SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=3.0 PACEthe frequency for hill addition=100 LABELa label for the action so that its output can be referenced in the input to other actions=restraint 
 FILE a file in which the list of added hills is stored=HILLS
... METAD

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=20 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=20

ENDPLUMEDTerminate plumed input. More details
Quantity	Type	Description
N	atoms	indices of atoms specified in GROUP
Quantity	Type	Description
O	atoms	indices of atoms specified in GROUP
Quantity	Type	Description
H	atoms	indices of atoms specified in GROUP
PLUMED-NEST

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