Project ID: plumID:19.082
Source: Ammonia_borane/4.H2_release/NH4+/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
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
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
bn1The GROUP action with label bn1 calculates the following quantities:| Quantity | Type | Description |
| bn1 | 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=1-128:16,3-128:16
bn2The GROUP action with label bn2 calculates the following quantities:| Quantity | Type | Description |
| bn2 | 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=2-128:16,4-128:16
cnHBThe COORDINATIONNUMBER action with label cnHB calculates the following quantities:| Quantity | Type | Description |
| cnHB | vector | the coordination numbers of the specified atoms |
| cnHB_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=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 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=1.8 NN=6 MM=12} MAXcalculate the maximum value={BETA=0.02}
# cnHB: COORDINATIONNUMBER SPECIESA=hb SPECIESB=b SWITCH={RATIONAL D_0=0.0 R_0=1.8 NN=6 MM=12} MAX={BETA=0.02}
cnHB_grpThe GROUP action with label cnHB_grp calculates the following quantities:| Quantity | Type | Description |
| cnHB_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
cnHB_matThe CONTACT_MATRIX action with label cnHB_mat calculates the following quantities:| Quantity | Type | Description |
| cnHB_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 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=1.8 NN=6 MM=12}
cnHB_onesThe CONSTANT action with label cnHB_ones calculates the following quantities:| Quantity | Type | Description |
| cnHB_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
cnHBThe MATRIX_VECTOR_PRODUCT action with label cnHB calculates the following quantities:| Quantity | Type | Description |
| cnHB | 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=cnHB_mat,cnHB_ones
cnHB_caverageThe MEAN action with label cnHB_caverage calculates the following quantities:| Quantity | Type | Description |
| cnHB_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=cnHB PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cnHB_me_maxThe CUSTOM action with label cnHB_me_max calculates the following quantities:| Quantity | Type | Description |
| cnHB_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=cnHB 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
cnHB_mec_maxThe SUM action with label cnHB_mec_max calculates the following quantities:| Quantity | Type | Description |
| cnHB_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=cnHB_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cnHB_maxThe CUSTOM action with label cnHB_max calculates the following quantities:| Quantity | Type | Description |
| cnHB_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cnHB_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 --- cnHHThe COORDINATIONNUMBER action with label cnHH calculates the following quantities:| Quantity | Type | Description |
| cnHH | vector | the coordination numbers of the specified atoms |
| cnHH_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=hn SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=hb 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.={GAUSSIAN R_0=0.2 D_0=0.8 } MAXcalculate the maximum value={BETA=0.02}
# cnHH: COORDINATIONNUMBER SPECIESA=hn SPECIESB=hb SWITCH={GAUSSIAN R_0=0.2 D_0=0.8 } MAX={BETA=0.02}
cnHH_grpThe GROUP action with label cnHH_grp calculates the following quantities:| Quantity | Type | Description |
| cnHH_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
cnHH_matThe CONTACT_MATRIX action with label cnHH_mat calculates the following quantities:| Quantity | Type | Description |
| cnHH_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=hb 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.={GAUSSIAN R_0=0.2 D_0=0.8 }
cnHH_onesThe CONSTANT action with label cnHH_ones calculates the following quantities:| Quantity | Type | Description |
| cnHH_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
cnHHThe MATRIX_VECTOR_PRODUCT action with label cnHH calculates the following quantities:| Quantity | Type | Description |
| cnHH | 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=cnHH_mat,cnHH_ones
cnHH_caverageThe MEAN action with label cnHH_caverage calculates the following quantities:| Quantity | Type | Description |
| cnHH_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=cnHH PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cnHH_me_maxThe CUSTOM action with label cnHH_me_max calculates the following quantities:| Quantity | Type | Description |
| cnHH_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=cnHH 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
cnHH_mec_maxThe SUM action with label cnHH_mec_max calculates the following quantities:| Quantity | Type | Description |
| cnHH_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=cnHH_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cnHH_maxThe CUSTOM action with label cnHH_max calculates the following quantities:| Quantity | Type | Description |
| cnHH_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cnHH_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 --- EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=cnHH.max FILEthe name of the file containing the external potential=ext_bias.dat LABELa label for the action so that its output can be referenced in the input to other actions=externalThe EXTERNAL action with label external calculates the following quantities:| Quantity | Type | Description |
| external.bias | scalar | the instantaneous value of the bias potential |
EXTERNALCalculate a restraint that is defined on a grid that is read during start up This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=cnHH.max FILEthe name of the file containing the external potential=ext_bias.dat LABELa label for the action so that its output can be referenced in the input to other actions=external SCALE a factor that multiplies the external potential, useful to invert free energies=1.0
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=cnHH.max SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=4000 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=400 BIASFACTORuse well tempered metadynamics and use this bias factor=10 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 |
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=cnHH.max SIGMAthe widths of the Gaussian hills=0.05 HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=4000 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=400 BIASFACTORuse well tempered metadynamics and use this bias factor=10 LABELa label for the action so that its output can be referenced in the input to other actions=restraint FILE a file in which the list of added hills is stored=HILLS
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
