Project ID: plumID:19.082
Source: Ammonia_borane/2.AaDB_to_AB2/PAB/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=5-128:16,6-128:16,7-128:16,8-128:16,9-128:16,10-128:16,11-128:16,12-128:16,13-128:16,14-128:16,15-128:16,16-128:16
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=3-128:16,4-128:16
bThe GROUP action with label b calculates the following quantities:| Quantity | Type | Description |
| b | 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=1-128:16,2-128:16
hbThe GROUP action with label hb calculates the following quantities:| Quantity | Type | Description |
| hb | 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=7-128:16,8-128:16,13-128:16,14-128:16,15-128:16,16-128:16
hnThe GROUP action with label hn calculates the following quantities:| Quantity | Type | Description |
| hn | 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=5-128:16,6-128:16,9-128:16,10-128:16,11-128:16,12-128:16
bm2The GROUP action with label bm2 calculates the following quantities:| Quantity | Type | Description |
| bm2 | 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=1-128:16,18-128:16
nm4The GROUP action with label nm4 calculates the following quantities:| Quantity | Type | Description |
| nm4 | 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=3-128:16,20-128:16
bbinterThe COORDINATIONNUMBER action with label bbinter calculates the following quantities:| Quantity | Type | Description |
| bbinter | vector | the coordination numbers of the specified atoms |
| bbinter_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 SPECIESAthe list of atoms for which the symmetry function is being calculated=2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=bm2 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=2.5 NN=6 MM=12} MEAN calculate the mean of all the quantities
# bbinter: COORDINATIONNUMBER SPECIESA=2 SPECIESB=bm2 SWITCH={RATIONAL D_0=0.0 R_0=2.5 NN=6 MM=12} MEAN
bbinter_grpThe GROUP action with label bbinter_grp calculates the following quantities:| Quantity | Type | Description |
| bbinter_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=2
bbinter_matThe CONTACT_MATRIX action with label bbinter_mat calculates the following quantities:| Quantity | Type | Description |
| bbinter_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=2 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=bm2 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=2.5 NN=6 MM=12}
bbinter_onesThe CONSTANT action with label bbinter_ones calculates the following quantities:| Quantity | Type | Description |
| bbinter_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=15
bbinterThe MATRIX_VECTOR_PRODUCT action with label bbinter calculates the following quantities:| Quantity | Type | Description |
| bbinter | 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=bbinter_mat,bbinter_ones
bbinter_caverageThe MEAN action with label bbinter_caverage calculates the following quantities:| Quantity | Type | Description |
| bbinter_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=bbinter PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bbinter_meanThe MEAN action with label bbinter_mean calculates the following quantities:| Quantity | Type | Description |
| bbinter_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=bbinter PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- nninterThe COORDINATIONNUMBER action with label nninter calculates the following quantities:| Quantity | Type | Description |
| nninter | vector | the coordination numbers of the specified atoms |
| nninter_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 SPECIESAthe list of atoms for which the symmetry function is being calculated=4 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=nm4 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=2.5 NN=7 MM=14} MEAN calculate the mean of all the quantities
# nninter: COORDINATIONNUMBER SPECIESA=4 SPECIESB=nm4 SWITCH={RATIONAL D_0=0.0 R_0=2.5 NN=7 MM=14} MEAN
nninter_grpThe GROUP action with label nninter_grp calculates the following quantities:| Quantity | Type | Description |
| nninter_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=4
nninter_matThe CONTACT_MATRIX action with label nninter_mat calculates the following quantities:| Quantity | Type | Description |
| nninter_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=4 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=nm4 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=2.5 NN=7 MM=14}
nninter_onesThe CONSTANT action with label nninter_ones calculates the following quantities:| Quantity | Type | Description |
| nninter_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=15
nninterThe MATRIX_VECTOR_PRODUCT action with label nninter calculates the following quantities:| Quantity | Type | Description |
| nninter | 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=nninter_mat,nninter_ones
nninter_caverageThe MEAN action with label nninter_caverage calculates the following quantities:| Quantity | Type | Description |
| nninter_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=nninter PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nninter_meanThe MEAN action with label nninter_mean calculates the following quantities:| Quantity | Type | Description |
| nninter_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=nninter PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- bhbridgeThe COORDINATIONNUMBER action with label bhbridge calculates the following quantities:| Quantity | Type | Description |
| bhbridge | vector | the coordination numbers of the specified atoms |
| bhbridge_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 and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=hb SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=b R_0The r_0 parameter of the switching function=1.9 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.02}
bhbridge: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=hb SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=b R_0The r_0 parameter of the switching function=1.9 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.02} D_0 The d_0 parameter of the switching function=0.0
# bhbridge: COORDINATIONNUMBER SPECIESA=hb SPECIESB=b R_0=1.9 NN=6 MM=12 MAX={BETA=0.02}
bhbridge_grpThe GROUP action with label bhbridge_grp calculates the following quantities:| Quantity | Type | Description |
| bhbridge_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=hb
bhbridge_matThe CONTACT_MATRIX action with label bhbridge_mat calculates the following quantities:| Quantity | Type | Description |
| bhbridge_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=hb 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=b R_0The r_0 parameter of the switching function=1.9 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
bhbridge_onesThe CONSTANT action with label bhbridge_ones calculates the following quantities:| Quantity | Type | Description |
| bhbridge_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=16
bhbridgeThe MATRIX_VECTOR_PRODUCT action with label bhbridge calculates the following quantities:| Quantity | Type | Description |
| bhbridge | 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=bhbridge_mat,bhbridge_ones
bhbridge_caverageThe MEAN action with label bhbridge_caverage calculates the following quantities:| Quantity | Type | Description |
| bhbridge_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=bhbridge PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bhbridge_me_maxThe CUSTOM action with label bhbridge_me_max calculates the following quantities:| Quantity | Type | Description |
| bhbridge_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=bhbridge 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
bhbridge_mec_maxThe SUM action with label bhbridge_mec_max calculates the following quantities:| Quantity | Type | Description |
| bhbridge_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=bhbridge_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bhbridge_maxThe CUSTOM action with label bhbridge_max calculates the following quantities:| Quantity | Type | Description |
| bhbridge_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=bhbridge_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 --- nhbridgeThe COORDINATIONNUMBER action with label nhbridge calculates the following quantities:| Quantity | Type | Description |
| nhbridge | vector | the coordination numbers of the specified atoms |
| nhbridge_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 and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=hn SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=n R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.02}
nhbridge: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=hn SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=n R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MAXcalculate the maximum value={BETA=0.02} D_0 The d_0 parameter of the switching function=0.0
# nhbridge: COORDINATIONNUMBER SPECIESA=hn SPECIESB=n R_0=1.6 NN=6 MM=12 MAX={BETA=0.02}
nhbridge_grpThe GROUP action with label nhbridge_grp calculates the following quantities:| Quantity | Type | Description |
| nhbridge_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=hn
nhbridge_matThe CONTACT_MATRIX action with label nhbridge_mat calculates the following quantities:| Quantity | Type | Description |
| nhbridge_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=hn 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 R_0The r_0 parameter of the switching function=1.6 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12
nhbridge_onesThe CONSTANT action with label nhbridge_ones calculates the following quantities:| Quantity | Type | Description |
| nhbridge_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=16
nhbridgeThe MATRIX_VECTOR_PRODUCT action with label nhbridge calculates the following quantities:| Quantity | Type | Description |
| nhbridge | 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=nhbridge_mat,nhbridge_ones
nhbridge_caverageThe MEAN action with label nhbridge_caverage calculates the following quantities:| Quantity | Type | Description |
| nhbridge_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=nhbridge PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nhbridge_me_maxThe CUSTOM action with label nhbridge_me_max calculates the following quantities:| Quantity | Type | Description |
| nhbridge_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=nhbridge 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
nhbridge_mec_maxThe SUM action with label nhbridge_mec_max calculates the following quantities:| Quantity | Type | Description |
| nhbridge_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=nhbridge_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nhbridge_maxThe CUSTOM action with label nhbridge_max calculates the following quantities:| Quantity | Type | Description |
| nhbridge_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=nhbridge_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 --- nhcoordThe COORDINATIONNUMBER action with label nhcoord calculates the following quantities:| Quantity | Type | Description |
| nhcoord | vector | the coordination numbers of the specified atoms |
| nhcoord_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 and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=4 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=hn R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =7 MM The m parameter of the switching function; 0 implies 2*NN=14 MEAN calculate the mean of all the quantities
nhcoord: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=4 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=hn R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =7 MM The m parameter of the switching function; 0 implies 2*NN=14 MEAN calculate the mean of all the quantities D_0 The d_0 parameter of the switching function=0.0
# nhcoord: COORDINATIONNUMBER SPECIESA=4 SPECIESB=hn R_0=1.6 NN=7 MM=14 MEAN
nhcoord_grpThe GROUP action with label nhcoord_grp calculates the following quantities:| Quantity | Type | Description |
| nhcoord_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=4
nhcoord_matThe CONTACT_MATRIX action with label nhcoord_mat calculates the following quantities:| Quantity | Type | Description |
| nhcoord_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=4 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=hn R_0The r_0 parameter of the switching function=1.6 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =7 MM The m parameter of the switching function; 0 implies 2*NN=14
nhcoord_onesThe CONSTANT action with label nhcoord_ones calculates the following quantities:| Quantity | Type | Description |
| nhcoord_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=48
nhcoordThe MATRIX_VECTOR_PRODUCT action with label nhcoord calculates the following quantities:| Quantity | Type | Description |
| nhcoord | 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=nhcoord_mat,nhcoord_ones
nhcoord_caverageThe MEAN action with label nhcoord_caverage calculates the following quantities:| Quantity | Type | Description |
| nhcoord_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=nhcoord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nhcoord_meanThe MEAN action with label nhcoord_mean calculates the following quantities:| Quantity | Type | Description |
| nhcoord_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=nhcoord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- bhcoordThe COORDINATIONNUMBER action with label bhcoord calculates the following quantities:| Quantity | Type | Description |
| bhcoord | vector | the coordination numbers of the specified atoms |
| bhcoord_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 and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=hb R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =7 MM The m parameter of the switching function; 0 implies 2*NN=14 MEAN calculate the mean of all the quantities
bhcoord: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=hb R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =7 MM The m parameter of the switching function; 0 implies 2*NN=14 MEAN calculate the mean of all the quantities D_0 The d_0 parameter of the switching function=0.0
# bhcoord: COORDINATIONNUMBER SPECIESA=2 SPECIESB=hb R_0=1.8 NN=7 MM=14 MEAN
bhcoord_grpThe GROUP action with label bhcoord_grp calculates the following quantities:| Quantity | Type | Description |
| bhcoord_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=2
bhcoord_matThe CONTACT_MATRIX action with label bhcoord_mat calculates the following quantities:| Quantity | Type | Description |
| bhcoord_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=2 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=hb R_0The r_0 parameter of the switching function=1.8 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =7 MM The m parameter of the switching function; 0 implies 2*NN=14
bhcoord_onesThe CONSTANT action with label bhcoord_ones calculates the following quantities:| Quantity | Type | Description |
| bhcoord_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=48
bhcoordThe MATRIX_VECTOR_PRODUCT action with label bhcoord calculates the following quantities:| Quantity | Type | Description |
| bhcoord | 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=bhcoord_mat,bhcoord_ones
bhcoord_caverageThe MEAN action with label bhcoord_caverage calculates the following quantities:| Quantity | Type | Description |
| bhcoord_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=bhcoord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bhcoord_meanThe MEAN action with label bhcoord_mean calculates the following quantities:| Quantity | Type | Description |
| bhcoord_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=bhcoord 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=bbinter.mean COEFFICIENTS the coefficients of the arguments in your function=0.8107 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=nninter.mean COEFFICIENTS the coefficients of the arguments in your function=1.1786 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=bhbridge.max COEFFICIENTS the coefficients of the arguments in your function=0.4960 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=nhbridge.max COEFFICIENTS the coefficients of the arguments in your function=0.6050 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=nhcoord.mean COEFFICIENTS the coefficients of the arguments in your function=0.2545 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=bhcoord.mean COEFFICIENTS the coefficients of the arguments in your function=0.2388 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sdg1The COMBINE action with label sdg1 calculates the following quantities:| Quantity | Type | Description |
| sdg1 | 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 COEFFICIENTS the coefficients of the arguments in your function=-0.0481,-0.0473,-0.1976,-0.2464,0.9415,0.0959 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sdg2The COMBINE action with label sdg2 calculates the following quantities:| Quantity | Type | Description |
| sdg2 | 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 COEFFICIENTS the coefficients of the arguments in your function=0.6319,-0.0329,-0.2130,-0.0029,0.4767,-0.5719 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
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=sdg1,sdg2 SIGMAthe widths of the Gaussian hills=0.03,0.03 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=100 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=400 BIASFACTORuse well tempered metadynamics and use this bias factor=8 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=4
WALKERS_IDwalker id=3
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=sdg1,sdg2 SIGMAthe widths of the Gaussian hills=0.03,0.03 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=100 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=400 BIASFACTORuse well tempered metadynamics and use this bias factor=8 LABELa label for the action so that its output can be referenced in the input to other actions=restraint
WALKERS_Nnumber of walkers=4
WALKERS_IDwalker id=3
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=1 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=1
ENDPLUMEDTerminate plumed input. More details
