PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:19.083
Source: Reaction_discovery/2.ICl/step1/B/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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

The UNITS action with label  calculates somethingHThe 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=1,2
IThe GROUP action with label I calculates the following quantities: Quantity    Type    Description  
I 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=3,5
ClThe GROUP action with label Cl calculates the following quantities: Quantity    Type    Description  
Cl 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=4,6

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=2
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 --- IIThe COORDINATIONNUMBER action with label II calculates the following quantities: Quantity    Type    Description  
II vector the coordination numbers of the specified atoms
II_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=I 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=3.0 NN=6 MM=8} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# II: COORDINATIONNUMBER SPECIES=I SWITCH={RATIONAL D_0=0.0 R_0=3.0 NN=6 MM=8} MEAN
# as follows (Click the red comment above to revert to the short version of the input):
II_grpThe GROUP action with label II_grp calculates the following quantities: Quantity    Type    Description  
II_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=I
II_matThe CONTACT_MATRIX action with label II_mat calculates the following quantities: Quantity    Type    Description  
II_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=I 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=3.0 NN=6 MM=8}
II_onesThe CONSTANT action with label II_ones calculates the following quantities: Quantity    Type    Description  
II_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
IIThe MATRIX_VECTOR_PRODUCT action with label II calculates the following quantities: Quantity    Type    Description  
II 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=II_mat,II_ones
II_caverageThe MEAN action with label II_caverage calculates the following quantities: Quantity    Type    Description  
II_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=II PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
II_meanThe MEAN action with label II_mean calculates the following quantities: Quantity    Type    Description  
II_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=II PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- ClClThe COORDINATIONNUMBER action with label ClCl calculates the following quantities: Quantity    Type    Description  
ClCl vector the coordination numbers of the specified atoms
ClCl_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=Cl 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=2.3 NN=6 MM=8} MEAN calculate the mean of all the quantities
# PLUMED interprets the command:
# ClCl: COORDINATIONNUMBER SPECIES=Cl SWITCH={RATIONAL D_0=0.0 R_0=2.3 NN=6 MM=8} MEAN
# as follows (Click the red comment above to revert to the short version of the input):
ClCl_grpThe GROUP action with label ClCl_grp calculates the following quantities: Quantity    Type    Description  
ClCl_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=Cl
ClCl_matThe CONTACT_MATRIX action with label ClCl_mat calculates the following quantities: Quantity    Type    Description  
ClCl_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=Cl 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=2.3 NN=6 MM=8}
ClCl_onesThe CONSTANT action with label ClCl_ones calculates the following quantities: Quantity    Type    Description  
ClCl_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
ClClThe MATRIX_VECTOR_PRODUCT action with label ClCl calculates the following quantities: Quantity    Type    Description  
ClCl 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=ClCl_mat,ClCl_ones
ClCl_caverageThe MEAN action with label ClCl_caverage calculates the following quantities: Quantity    Type    Description  
ClCl_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=ClCl PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ClCl_meanThe MEAN action with label ClCl_mean calculates the following quantities: Quantity    Type    Description  
ClCl_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=ClCl PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- HClThe COORDINATIONNUMBER action with label HCl calculates the following quantities: Quantity    Type    Description  
HCl vector the coordination numbers of the specified atoms
HCl_min scalar the minimum colvar
HCl_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=Cl 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:
# HCl: COORDINATIONNUMBER SPECIESA=H SPECIESB=Cl 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):
HCl_grpThe GROUP action with label HCl_grp calculates the following quantities: Quantity    Type    Description  
HCl_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
HCl_matThe CONTACT_MATRIX action with label HCl_mat calculates the following quantities: Quantity    Type    Description  
HCl_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=Cl 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}
HCl_onesThe CONSTANT action with label HCl_ones calculates the following quantities: Quantity    Type    Description  
HCl_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
HClThe MATRIX_VECTOR_PRODUCT action with label HCl calculates the following quantities: Quantity    Type    Description  
HCl 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=HCl_mat,HCl_ones
HCl_caverageThe MEAN action with label HCl_caverage calculates the following quantities: Quantity    Type    Description  
HCl_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=HCl PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
HCl_me_minThe CUSTOM action with label HCl_me_min calculates the following quantities: Quantity    Type    Description  
HCl_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=HCl 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
HCl_mec_minThe SUM action with label HCl_mec_min calculates the following quantities: Quantity    Type    Description  
HCl_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=HCl_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
HCl_minThe CUSTOM action with label HCl_min calculates the following quantities: Quantity    Type    Description  
HCl_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=HCl_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
HCl_me_maxThe CUSTOM action with label HCl_me_max calculates the following quantities: Quantity    Type    Description  
HCl_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=HCl 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
HCl_mec_maxThe SUM action with label HCl_mec_max calculates the following quantities: Quantity    Type    Description  
HCl_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=HCl_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
HCl_maxThe CUSTOM action with label HCl_max calculates the following quantities: Quantity    Type    Description  
HCl_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=HCl_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 --- ClHThe COORDINATIONNUMBER action with label ClH calculates the following quantities: Quantity    Type    Description  
ClH vector the coordination numbers of the specified atoms
ClH_min scalar the minimum colvar
ClH_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=Cl 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=1.6 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# ClH: COORDINATIONNUMBER SPECIESA=Cl SPECIESB=H 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):
ClH_grpThe GROUP action with label ClH_grp calculates the following quantities: Quantity    Type    Description  
ClH_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=Cl
ClH_matThe CONTACT_MATRIX action with label ClH_mat calculates the following quantities: Quantity    Type    Description  
ClH_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=Cl 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=1.6 NN=6 MM=8}
ClH_onesThe CONSTANT action with label ClH_ones calculates the following quantities: Quantity    Type    Description  
ClH_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
ClHThe MATRIX_VECTOR_PRODUCT action with label ClH calculates the following quantities: Quantity    Type    Description  
ClH 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=ClH_mat,ClH_ones
ClH_caverageThe MEAN action with label ClH_caverage calculates the following quantities: Quantity    Type    Description  
ClH_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=ClH PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ClH_me_minThe CUSTOM action with label ClH_me_min calculates the following quantities: Quantity    Type    Description  
ClH_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=ClH 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
ClH_mec_minThe SUM action with label ClH_mec_min calculates the following quantities: Quantity    Type    Description  
ClH_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=ClH_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ClH_minThe CUSTOM action with label ClH_min calculates the following quantities: Quantity    Type    Description  
ClH_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ClH_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
ClH_me_maxThe CUSTOM action with label ClH_me_max calculates the following quantities: Quantity    Type    Description  
ClH_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=ClH 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
ClH_mec_maxThe SUM action with label ClH_mec_max calculates the following quantities: Quantity    Type    Description  
ClH_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=ClH_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ClH_maxThe CUSTOM action with label ClH_max calculates the following quantities: Quantity    Type    Description  
ClH_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ClH_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 --- HIThe COORDINATIONNUMBER action with label HI calculates the following quantities: Quantity    Type    Description  
HI vector the coordination numbers of the specified atoms
HI_min scalar the minimum colvar
HI_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=I 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=1.9 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# HI: COORDINATIONNUMBER SPECIESA=H SPECIESB=I SWITCH={RATIONAL D_0=0.0 R_0=1.9 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):
HI_grpThe GROUP action with label HI_grp calculates the following quantities: Quantity    Type    Description  
HI_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
HI_matThe CONTACT_MATRIX action with label HI_mat calculates the following quantities: Quantity    Type    Description  
HI_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=I 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=1.9 NN=6 MM=8}
HI_onesThe CONSTANT action with label HI_ones calculates the following quantities: Quantity    Type    Description  
HI_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
HIThe MATRIX_VECTOR_PRODUCT action with label HI calculates the following quantities: Quantity    Type    Description  
HI 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=HI_mat,HI_ones
HI_caverageThe MEAN action with label HI_caverage calculates the following quantities: Quantity    Type    Description  
HI_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=HI PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
HI_me_minThe CUSTOM action with label HI_me_min calculates the following quantities: Quantity    Type    Description  
HI_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=HI 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
HI_mec_minThe SUM action with label HI_mec_min calculates the following quantities: Quantity    Type    Description  
HI_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=HI_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
HI_minThe CUSTOM action with label HI_min calculates the following quantities: Quantity    Type    Description  
HI_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=HI_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
HI_me_maxThe CUSTOM action with label HI_me_max calculates the following quantities: Quantity    Type    Description  
HI_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=HI 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
HI_mec_maxThe SUM action with label HI_mec_max calculates the following quantities: Quantity    Type    Description  
HI_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=HI_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
HI_maxThe CUSTOM action with label HI_max calculates the following quantities: Quantity    Type    Description  
HI_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=HI_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 --- IHThe COORDINATIONNUMBER action with label IH calculates the following quantities: Quantity    Type    Description  
IH vector the coordination numbers of the specified atoms
IH_min scalar the minimum colvar
IH_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=I 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=1.9 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# IH: COORDINATIONNUMBER SPECIESA=I SPECIESB=H SWITCH={RATIONAL D_0=0.0 R_0=1.9 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):
IH_grpThe GROUP action with label IH_grp calculates the following quantities: Quantity    Type    Description  
IH_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=I
IH_matThe CONTACT_MATRIX action with label IH_mat calculates the following quantities: Quantity    Type    Description  
IH_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=I 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=1.9 NN=6 MM=8}
IH_onesThe CONSTANT action with label IH_ones calculates the following quantities: Quantity    Type    Description  
IH_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
IHThe MATRIX_VECTOR_PRODUCT action with label IH calculates the following quantities: Quantity    Type    Description  
IH 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=IH_mat,IH_ones
IH_caverageThe MEAN action with label IH_caverage calculates the following quantities: Quantity    Type    Description  
IH_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=IH PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
IH_me_minThe CUSTOM action with label IH_me_min calculates the following quantities: Quantity    Type    Description  
IH_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=IH 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
IH_mec_minThe SUM action with label IH_mec_min calculates the following quantities: Quantity    Type    Description  
IH_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=IH_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
IH_minThe CUSTOM action with label IH_min calculates the following quantities: Quantity    Type    Description  
IH_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=IH_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
IH_me_maxThe CUSTOM action with label IH_me_max calculates the following quantities: Quantity    Type    Description  
IH_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=IH 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
IH_mec_maxThe SUM action with label IH_mec_max calculates the following quantities: Quantity    Type    Description  
IH_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=IH_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
IH_maxThe CUSTOM action with label IH_max calculates the following quantities: Quantity    Type    Description  
IH_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=IH_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 --- IClThe COORDINATIONNUMBER action with label ICl calculates the following quantities: Quantity    Type    Description  
ICl vector the coordination numbers of the specified atoms
ICl_min scalar the minimum colvar
ICl_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=I SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Cl 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=2.6 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# ICl: COORDINATIONNUMBER SPECIESA=I SPECIESB=Cl SWITCH={RATIONAL D_0=0.0 R_0=2.6 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):
ICl_grpThe GROUP action with label ICl_grp calculates the following quantities: Quantity    Type    Description  
ICl_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=I
ICl_matThe CONTACT_MATRIX action with label ICl_mat calculates the following quantities: Quantity    Type    Description  
ICl_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=I 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=Cl 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=2.6 NN=6 MM=8}
ICl_onesThe CONSTANT action with label ICl_ones calculates the following quantities: Quantity    Type    Description  
ICl_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
IClThe MATRIX_VECTOR_PRODUCT action with label ICl calculates the following quantities: Quantity    Type    Description  
ICl 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=ICl_mat,ICl_ones
ICl_caverageThe MEAN action with label ICl_caverage calculates the following quantities: Quantity    Type    Description  
ICl_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=ICl PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ICl_me_minThe CUSTOM action with label ICl_me_min calculates the following quantities: Quantity    Type    Description  
ICl_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=ICl 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
ICl_mec_minThe SUM action with label ICl_mec_min calculates the following quantities: Quantity    Type    Description  
ICl_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=ICl_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ICl_minThe CUSTOM action with label ICl_min calculates the following quantities: Quantity    Type    Description  
ICl_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ICl_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
ICl_me_maxThe CUSTOM action with label ICl_me_max calculates the following quantities: Quantity    Type    Description  
ICl_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=ICl 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
ICl_mec_maxThe SUM action with label ICl_mec_max calculates the following quantities: Quantity    Type    Description  
ICl_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=ICl_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ICl_maxThe CUSTOM action with label ICl_max calculates the following quantities: Quantity    Type    Description  
ICl_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ICl_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 --- ClIThe COORDINATIONNUMBER action with label ClI calculates the following quantities: Quantity    Type    Description  
ClI vector the coordination numbers of the specified atoms
ClI_min scalar the minimum colvar
ClI_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=Cl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=I 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=2.6 NN=6 MM=8} MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.02}
# PLUMED interprets the command:
# ClI: COORDINATIONNUMBER SPECIESA=Cl SPECIESB=I SWITCH={RATIONAL D_0=0.0 R_0=2.6 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):
ClI_grpThe GROUP action with label ClI_grp calculates the following quantities: Quantity    Type    Description  
ClI_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=Cl
ClI_matThe CONTACT_MATRIX action with label ClI_mat calculates the following quantities: Quantity    Type    Description  
ClI_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=Cl 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=I 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=2.6 NN=6 MM=8}
ClI_onesThe CONSTANT action with label ClI_ones calculates the following quantities: Quantity    Type    Description  
ClI_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
ClIThe MATRIX_VECTOR_PRODUCT action with label ClI calculates the following quantities: Quantity    Type    Description  
ClI 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=ClI_mat,ClI_ones
ClI_caverageThe MEAN action with label ClI_caverage calculates the following quantities: Quantity    Type    Description  
ClI_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=ClI PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ClI_me_minThe CUSTOM action with label ClI_me_min calculates the following quantities: Quantity    Type    Description  
ClI_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=ClI 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
ClI_mec_minThe SUM action with label ClI_mec_min calculates the following quantities: Quantity    Type    Description  
ClI_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=ClI_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ClI_minThe CUSTOM action with label ClI_min calculates the following quantities: Quantity    Type    Description  
ClI_min scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ClI_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
ClI_me_maxThe CUSTOM action with label ClI_me_max calculates the following quantities: Quantity    Type    Description  
ClI_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=ClI 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
ClI_mec_maxThe SUM action with label ClI_mec_max calculates the following quantities: Quantity    Type    Description  
ClI_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=ClI_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ClI_maxThe CUSTOM action with label ClI_max calculates the following quantities: Quantity    Type    Description  
ClI_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ClI_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=1.0232 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=II.mean COEFFICIENTS the coefficients of the arguments in your function=1.1790 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=ClCl.mean COEFFICIENTS the coefficients of the arguments in your function=2.1364 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=HCl.max COEFFICIENTS the coefficients of the arguments in your function=0.7082 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=HCl.min COEFFICIENTS the coefficients of the arguments in your function=0.8116 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=ClH.max COEFFICIENTS the coefficients of the arguments in your function=0.6879 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=ClH.min COEFFICIENTS the coefficients of the arguments in your function=0.7994 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=HI.max COEFFICIENTS the coefficients of the arguments in your function=1.1615 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=HI.min COEFFICIENTS the coefficients of the arguments in your function=1.7905 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=IH.max COEFFICIENTS the coefficients of the arguments in your function=1.2714 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=IH.min COEFFICIENTS the coefficients of the arguments in your function=1.6849 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=ICl.max COEFFICIENTS the coefficients of the arguments in your function=0.8310 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=ICl.min COEFFICIENTS the coefficients of the arguments in your function=0.9355 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=ClI.max COEFFICIENTS the coefficients of the arguments in your function=0.8257 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=ClI.min COEFFICIENTS the coefficients of the arguments in your function=0.9352 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

sdg1fullThe COMBINE action with label sdg1full calculates the following quantities: Quantity    Type    Description  
sdg1full 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=0.6688,-0.0250,-0.2889,-0.3031,-0.5252,0.2230,-0.1102,-0.0069,0.0331,-0.0102,-0.0103,0.1540,-0.0335,0.0968,0.0583 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

svd13m1The COMBINE action with label svd13m1 calculates the following quantities: Quantity    Type    Description  
svd13m1 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=-0.4446,0.0049,0.0288,0.1219,0.0686,0.0886,0.0323,0.1243,0.0676,-0.0530,-0.0781,0.4969,0.3439,-0.4511,-0.4189 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
svd13m2The COMBINE action with label svd13m2 calculates the following quantities: Quantity    Type    Description  
svd13m2 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=-0.0450,0.0427,0.2969,-0.4559,0.4762,-0.0061,0.1473,-0.3869,-0.1632,0.2848,0.2102,-0.0487,0.2557,-0.2622,-0.1160 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
svd11m1The COMBINE action with label svd11m1 calculates the following quantities: Quantity    Type    Description  
svd11m1 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=-0.8075,0.0186,0.2521,0.1816,0.2349,0.0562,0.3967,0.0364,-0.0429,0.0242,-0.0034,-0.1252,-0.0373,-0.1007,-0.0662 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
svd11m2The COMBINE action with label svd11m2 calculates the following quantities: Quantity    Type    Description  
svd11m2 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=0.1102,0.1135,0.5696,-0.1055,0.2089,-0.1612,0.2692,-0.2625,0.2177,-0.1559,-0.0388,-0.4719,0.2804,-0.2171,0.0822 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
svd9m1The COMBINE action with label svd9m1 calculates the following quantities: Quantity    Type    Description  
svd9m1 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=0.7820,-0.0074,-0.0974,-0.2334,0.0800,-0.1052,-0.1291,-0.2370,0.3061,-0.0213,-0.1431,-0.0234,0.2626,-0.0026,0.2235 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
svd9m2The COMBINE action with label svd9m2 calculates the following quantities: Quantity    Type    Description  
svd9m2 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=0.0079,-0.2227,0.0969,-0.0597,-0.3591,0.1200,-0.5246,0.4716,-0.4417,0.1350,0.2572,0.1127,-0.0455,0.0354,0.0322 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  

  
sdg1filter075The COMBINE action with label sdg1filter075 calculates the following quantities: Quantity    Type    Description  
sdg1filter075 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=-0.4916,0.0056,0.0378,0.2220,0.1772,0.0,-0.0576,-0.0072,0.0050,0.0775,0.0,0.4842,0.2992,-0.4425,-0.3835 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
sdg2filter075The COMBINE action with label sdg2filter075 calculates the following quantities: Quantity    Type    Description  
sdg2filter075 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=0.0269,-0.0375,-0.2456,0.3938,-0.3926,0.0,-0.1366,0.0201,-0.0019,0.0464,0.0,-0.1701,-0.5095,0.4204,0.3766 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
sdg1filter095The COMBINE action with label sdg1filter095 calculates the following quantities: Quantity    Type    Description  
sdg1filter095 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=0.7429,-0.0276,-0.3225,0.0,-0.4192,-0.0218,-0.3448,-0.0248,0.0316,0.0,-0.0045,0.1832,-0.0276,0.0958,0.0550 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
sdg1filter090The COMBINE action with label sdg1filter090 calculates the following quantities: Quantity    Type    Description  
sdg1filter090 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=0.7026,-0.0342,-0.3478,0.0,-0.3629,0.0,-0.3840,-0.0031,0.0186,0.0,-0.0052,0.2806,0.1303,0.0,-0.0945 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=0.7435,-0.0278,-0.3230,0.0052,-0.4295,-0.0315,-0.3276,-0.0540,0.0093,0.0297,0.0162,0.1870,-0.0130,0.0911,0.0412 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  
svd11The COMBINE action with label svd11 calculates the following quantities: Quantity    Type    Description  
svd11 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=0.7739,-0.0297,-0.3295,-0.1430,-0.2591,-0.0257,-0.3954,-0.0026,0.0093,0.0020,-0.0007,0.1858,-0.0170,0.0995,0.0471 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  

dHClThe DISTANCES action with label dHCl calculates the following quantities: Quantity    Type    Description  
dHCl vector the DISTANCES between the each pair of atoms that were specified
dHCl_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=H GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Cl MAXcalculate the maximum value={BETA=0.02} NOPBC ignore the periodic boundary conditions when calculating distances
# PLUMED interprets the command:
# dHCl: DISTANCES GROUPA=H GROUPB=Cl MAX={BETA=0.02} NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
dHClThe DISTANCE action with label dHCl calculates the following quantities: Quantity    Type    Description  
dHCl 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=1,4 ATOMS2the pair of atom that we are calculating the distance between=1,6 ATOMS3the pair of atom that we are calculating the distance between=2,4 ATOMS4the pair of atom that we are calculating the distance between=2,6
dHCl_me_maxThe CUSTOM action with label dHCl_me_max calculates the following quantities: Quantity    Type    Description  
dHCl_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=dHCl 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
dHCl_mec_maxThe SUM action with label dHCl_mec_max calculates the following quantities: Quantity    Type    Description  
dHCl_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=dHCl_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dHCl_maxThe CUSTOM action with label dHCl_max calculates the following quantities: Quantity    Type    Description  
dHCl_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dHCl_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 --- dHIThe DISTANCES action with label dHI calculates the following quantities: Quantity    Type    Description  
dHI vector the DISTANCES between the each pair of atoms that were specified
dHI_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=H GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=I MAXcalculate the maximum value={BETA=0.02} NOPBC ignore the periodic boundary conditions when calculating distances
# PLUMED interprets the command:
# dHI: DISTANCES GROUPA=H GROUPB=I MAX={BETA=0.02} NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
dHIThe DISTANCE action with label dHI calculates the following quantities: Quantity    Type    Description  
dHI 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=1,3 ATOMS2the pair of atom that we are calculating the distance between=1,5 ATOMS3the pair of atom that we are calculating the distance between=2,3 ATOMS4the pair of atom that we are calculating the distance between=2,5
dHI_me_maxThe CUSTOM action with label dHI_me_max calculates the following quantities: Quantity    Type    Description  
dHI_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=dHI 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
dHI_mec_maxThe SUM action with label dHI_mec_max calculates the following quantities: Quantity    Type    Description  
dHI_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=dHI_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dHI_maxThe CUSTOM action with label dHI_max calculates the following quantities: Quantity    Type    Description  
dHI_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dHI_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 --- dIClThe DISTANCES action with label dICl calculates the following quantities: Quantity    Type    Description  
dICl vector the DISTANCES between the each pair of atoms that were specified
dICl_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=I GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Cl MAXcalculate the maximum value={BETA=0.02} NOPBC ignore the periodic boundary conditions when calculating distances
# PLUMED interprets the command:
# dICl: DISTANCES GROUPA=I GROUPB=Cl MAX={BETA=0.02} NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
dIClThe DISTANCE action with label dICl calculates the following quantities: Quantity    Type    Description  
dICl 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=3,4 ATOMS2the pair of atom that we are calculating the distance between=3,6 ATOMS3the pair of atom that we are calculating the distance between=5,4 ATOMS4the pair of atom that we are calculating the distance between=5,6
dICl_me_maxThe CUSTOM action with label dICl_me_max calculates the following quantities: Quantity    Type    Description  
dICl_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=dICl 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
dICl_mec_maxThe SUM action with label dICl_mec_max calculates the following quantities: Quantity    Type    Description  
dICl_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=dICl_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dICl_maxThe CUSTOM action with label dICl_max calculates the following quantities: Quantity    Type    Description  
dICl_max scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dICl_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 --- wallHClThe UPPER_WALLS action with label wallHCl calculates the following quantities: Quantity    Type    Description  
wallHCl.bias scalar the instantaneous value of the bias potential
wallHCl.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=dHCl.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
wallHIThe UPPER_WALLS action with label wallHI calculates the following quantities: Quantity    Type    Description  
wallHI.bias scalar the instantaneous value of the bias potential
wallHI.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=dHI.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 
wallIClThe UPPER_WALLS action with label wallICl calculates the following quantities: Quantity    Type    Description  
wallICl.bias scalar the instantaneous value of the bias potential
wallICl.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=dICl.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=svd13m1,svd13m2 SIGMAthe widths of the Gaussian hills=0.05,0.05 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=100 BIASFACTORuse well tempered metadynamics and use this bias factor=60 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=400.0 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 
   WALKERS_Nnumber of walkers=3
   WALKERS_IDwalker id=1
   WALKERS_DIRshared directory with the hills files from all the walkers=../
   WALKERS_RSTRIDEstride for reading hills files=50
... 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=svd13m1,svd13m2 SIGMAthe widths of the Gaussian hills=0.05,0.05 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=100 BIASFACTORuse well tempered metadynamics and use this bias factor=60 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=400.0 LABELa label for the action so that its output can be referenced in the input to other actions=restraint 
   WALKERS_Nnumber of walkers=3
   WALKERS_IDwalker id=1
   WALKERS_DIRshared directory with the hills files from all the walkers=../
   WALKERS_RSTRIDEstride for reading hills files=50
 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
H	atoms	indices of atoms specified in GROUP
Quantity	Type	Description
I	atoms	indices of atoms specified in GROUP
PLUMED-NEST-TEST-SITE

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