Project ID: plumID:19.082
Source: Ammonia_borane/1.AB_to_AaDB/AaDB_bis/plumed.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
RESTARTActivate restart. More details
The RESTART action with label calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
hThe GROUP action with label h calculates the following quantities:| Quantity | Type | Description |
| h | atoms | indices of atoms specified in GROUP |
: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=5-128:16,6-128:16,7-128:16,8-128:16,9-128:16,10-128:16,11-128:16,12-128:16,13-128:16,14-128:16,15-128:16,16-128:16
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
bnintragThe COORDINATIONNUMBER action with label bnintrag calculates the following quantities:| Quantity | Type | Description |
| bnintrag | vector | the coordination numbers of the specified atoms |
| bnintrag_min | scalar | the minimum 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=b 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=2.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MINcalculate the minimum value={BETA=20.0}
bnintrag: 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=b 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=2.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=12 MINcalculate the minimum value={BETA=20.0} D_0 The d_0 parameter of the switching function=0.0
# bnintrag: COORDINATIONNUMBER SPECIESA=b SPECIESB=n R_0=2.0 NN=6 MM=12 MIN={BETA=20.0}
bnintrag_grpThe GROUP action with label bnintrag_grp calculates the following quantities:| Quantity | Type | Description |
| bnintrag_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=b
bnintrag_matThe CONTACT_MATRIX action with label bnintrag_mat calculates the following quantities:| Quantity | Type | Description |
| bnintrag_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=b 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=2.0 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
bnintrag_onesThe CONSTANT action with label bnintrag_ones calculates the following quantities:| Quantity | Type | Description |
| bnintrag_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
bnintragThe MATRIX_VECTOR_PRODUCT action with label bnintrag calculates the following quantities:| Quantity | Type | Description |
| bnintrag | 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=bnintrag_mat,bnintrag_ones
bnintrag_caverageThe MEAN action with label bnintrag_caverage calculates the following quantities:| Quantity | Type | Description |
| bnintrag_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=bnintrag PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bnintrag_me_minThe CUSTOM action with label bnintrag_me_min calculates the following quantities:| Quantity | Type | Description |
| bnintrag_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=bnintrag 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
bnintrag_mec_minThe SUM action with label bnintrag_mec_min calculates the following quantities:| Quantity | Type | Description |
| bnintrag_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=bnintrag_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bnintrag_minThe CUSTOM action with label bnintrag_min calculates the following quantities:| Quantity | Type | Description |
| bnintrag_min | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=bnintrag_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
# --- End of included input --- bnintranewThe COORDINATIONNUMBER action with label bnintranew calculates the following quantities:| Quantity | Type | Description |
| bnintranew | vector | the coordination numbers of the specified atoms |
| bnintranew_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=4 R_0The r_0 parameter of the switching function=2.2 NN The n parameter of the switching function =4 MM The m parameter of the switching function; 0 implies 2*NN=8 MEAN calculate the mean of all the quantities
bnintranew: 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=4 R_0The r_0 parameter of the switching function=2.2 NN The n parameter of the switching function =4 MM The m parameter of the switching function; 0 implies 2*NN=8 MEAN calculate the mean of all the quantities D_0 The d_0 parameter of the switching function=0.0
# bnintranew: COORDINATIONNUMBER SPECIESA=2 SPECIESB=4 R_0=2.2 NN=4 MM=8 MEAN
bnintranew_grpThe GROUP action with label bnintranew_grp calculates the following quantities:| Quantity | Type | Description |
| bnintranew_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
bnintranew_matThe CONTACT_MATRIX action with label bnintranew_mat calculates the following quantities:| Quantity | Type | Description |
| bnintranew_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=4 R_0The r_0 parameter of the switching function=2.2 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =4 MM The m parameter of the switching function; 0 implies 2*NN=8
bnintranew_onesThe CONSTANT action with label bnintranew_ones calculates the following quantities:| Quantity | Type | Description |
| bnintranew_ones | scalar | 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=1
bnintranewThe MATRIX_VECTOR_PRODUCT action with label bnintranew calculates the following quantities:| Quantity | Type | Description |
| bnintranew | 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=bnintranew_mat,bnintranew_ones
bnintranew_caverageThe MEAN action with label bnintranew_caverage calculates the following quantities:| Quantity | Type | Description |
| bnintranew_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=bnintranew PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bnintranew_meanThe MEAN action with label bnintranew_mean calculates the following quantities:| Quantity | Type | Description |
| bnintranew_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=bnintranew PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- bbinterThe COORDINATIONNUMBER action with label bbinter calculates the following quantities:| Quantity | Type | Description |
| bbinter | vector | the coordination numbers of the specified atoms |
| bbinter_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=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} MAXcalculate the maximum value={BETA=0.02}
# bbinter: COORDINATIONNUMBER SPECIESA=2 SPECIESB=bm2 SWITCH={RATIONAL D_0=0.0 R_0=2.5 NN=6 MM=12} MAX={BETA=0.02}
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_me_maxThe CUSTOM action with label bbinter_me_max calculates the following quantities:| Quantity | Type | Description |
| bbinter_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=bbinter 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
bbinter_mec_maxThe SUM action with label bbinter_mec_max calculates the following quantities:| Quantity | Type | Description |
| bbinter_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=bbinter_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
bbinter_maxThe CUSTOM action with label bbinter_max calculates the following quantities:| Quantity | Type | Description |
| bbinter_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=bbinter_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 --- 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 ---
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=bnintrag.min,bhbridge.max SIGMAthe widths of the Gaussian hills=0.075,0.075 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=16 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=1
... 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=bnintrag.min,bhbridge.max SIGMAthe widths of the Gaussian hills=0.075,0.075 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=16 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=1
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
