Project ID: plumID:25.004
Source: NH3_formation/plumed.dat
Originally used with PLUMED version: 2.9
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
# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=0.001
The UNITS action with label calculates somethingN2The GROUP action with label N2 calculates the following quantities:| Quantity | Type | Description |
| N2 | 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=755,756
HrThe GROUP action with label Hr calculates the following quantities:| Quantity | Type | Description |
| Hr | 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=759,760
cThe COORDINATIONNUMBER action with label c calculates the following quantities:| Quantity | Type | Description |
| c | vector | the coordination numbers of the specified atoms |
| c_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=N2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Hr 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 MAXcalculate the maximum value={BETA=0.05}
c: 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=N2 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=Hr 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 MAXcalculate the maximum value={BETA=0.05} D_0 The d_0 parameter of the switching function=0.0
# c: COORDINATIONNUMBER SPECIESA=N2 SPECIESB=Hr R_0=2.0 NN=6 MM=12 MAX={BETA=0.05}
c_grpThe GROUP action with label c_grp calculates the following quantities:| Quantity | Type | Description |
| c_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=N2
c_matThe CONTACT_MATRIX action with label c_mat calculates the following quantities:| Quantity | Type | Description |
| c_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=N2 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=Hr 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
c_onesThe CONSTANT action with label c_ones calculates the following quantities:| Quantity | Type | Description |
| c_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
cThe MATRIX_VECTOR_PRODUCT action with label c calculates the following quantities:| Quantity | Type | Description |
| c | 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=c_mat,c_ones
c_caverageThe MEAN action with label c_caverage calculates the following quantities:| Quantity | Type | Description |
| c_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=c PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c_me_maxThe CUSTOM action with label c_me_max calculates the following quantities:| Quantity | Type | Description |
| c_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=c FUNCthe function you wish to evaluate=exp(x/0.05) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c_mec_maxThe SUM action with label c_mec_max calculates the following quantities:| Quantity | Type | Description |
| c_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=c_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c_maxThe CUSTOM action with label c_max calculates the following quantities:| Quantity | Type | Description |
| c_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=c_mec_max FUNCthe function you wish to evaluate=0.05*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
dNHThe DISTANCES action with label dNH calculates the following quantities:| Quantity | Type | Description |
| dNH | vector | the DISTANCES between the each pair of atoms that were specified |
| dNH_min | scalar | the minimum 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=N2 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Hr MINcalculate the minimum value={BETA=20.0}
# dNH: DISTANCES GROUPA=N2 GROUPB=Hr MIN={BETA=20.0}
dNHThe DISTANCE action with label dNH calculates the following quantities:| Quantity | Type | Description |
| dNH | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=755,759 ATOMS2the pair of atom that we are calculating the distance between=755,760 ATOMS3the pair of atom that we are calculating the distance between=756,759 ATOMS4the pair of atom that we are calculating the distance between=756,760
dNH_me_minThe CUSTOM action with label dNH_me_min calculates the following quantities:| Quantity | Type | Description |
| dNH_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=dNH 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
dNH_mec_minThe SUM action with label dNH_mec_min calculates the following quantities:| Quantity | Type | Description |
| dNH_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=dNH_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNH_minThe CUSTOM action with label dNH_min calculates the following quantities:| Quantity | Type | Description |
| dNH_min | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNH_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 --- dNH1The DISTANCES action with label dNH1 calculates the following quantities:| Quantity | Type | Description |
| dNH1 | vector | the DISTANCES between the each pair of atoms that were specified |
| dNH1_min | scalar | the minimum colvar |
| dNH1_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=756 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Hr MINcalculate the minimum value={BETA=20.0} MAXcalculate the maximum value={BETA=0.05}
# dNH1: DISTANCES GROUPA=756 GROUPB=Hr MIN={BETA=20.0} MAX={BETA=0.05}
dNH1The DISTANCE action with label dNH1 calculates the following quantities:| Quantity | Type | Description |
| dNH1 | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=756,759 ATOMS2the pair of atom that we are calculating the distance between=756,760
dNH1_me_minThe CUSTOM action with label dNH1_me_min calculates the following quantities:| Quantity | Type | Description |
| dNH1_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=dNH1 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
dNH1_mec_minThe SUM action with label dNH1_mec_min calculates the following quantities:| Quantity | Type | Description |
| dNH1_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=dNH1_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNH1_minThe CUSTOM action with label dNH1_min calculates the following quantities:| Quantity | Type | Description |
| dNH1_min | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNH1_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
dNH1_me_maxThe CUSTOM action with label dNH1_me_max calculates the following quantities:| Quantity | Type | Description |
| dNH1_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=dNH1 FUNCthe function you wish to evaluate=exp(x/0.05) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNH1_mec_maxThe SUM action with label dNH1_mec_max calculates the following quantities:| Quantity | Type | Description |
| dNH1_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=dNH1_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dNH1_maxThe CUSTOM action with label dNH1_max calculates the following quantities:| Quantity | Type | Description |
| dNH1_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNH1_mec_max FUNCthe function you wish to evaluate=0.05*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
dHHThe DISTANCES action with label dHH calculates the following quantities:| Quantity | Type | Description |
| dHH | vector | the DISTANCES between the each pair of atoms that were specified |
| dHH_min | scalar | the minimum colvar |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPCalculate the distance between each distinct pair of atoms in the group=Hr MINcalculate the minimum value={BETA=20.0}
# dHH: DISTANCES GROUP=Hr MIN={BETA=20.0}
dHHThe DISTANCE action with label dHH calculates the following quantities:| Quantity | Type | Description |
| dHH | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=760,759
dHH_me_minThe CUSTOM action with label dHH_me_min calculates the following quantities:| Quantity | Type | Description |
| dHH_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=dHH 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
dHH_mec_minThe SUM action with label dHH_mec_min calculates the following quantities:| Quantity | Type | Description |
| dHH_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=dHH_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dHH_minThe CUSTOM action with label dHH_min calculates the following quantities:| Quantity | Type | Description |
| dHH_min | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dHH_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 ---
uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities:| Quantity | Type | Description |
| uwall1.bias | scalar | the instantaneous value of the bias potential |
| uwall1.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=dNH1.max ATthe positions of the wall=5.0 KAPPAthe force constant for the wall=200 EXP the powers for the walls=2.0
target1The CUSTOM action with label target1 calculates the following quantities:| Quantity | Type | Description |
| target1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dNH.min FUNCthe function you wish to evaluate=step(2-x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes1The OPES_METAD action with label opes1 calculates the following quantities:| Quantity | Type | Description |
| opes1.bias | scalar | the instantaneous value of the bias potential |
| opes1.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes1.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes1.neff | scalar | effective sample size |
| opes1.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=dNH1.min
FILE a file in which the list of all deposited kernels is stored=Kernels1.data
TEMP temperature=550
PACEthe frequency for kernel deposition=200
BARRIERthe free energy barrier to be overcome=40
RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=target1
... OPES_METAD
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes1
ARGthe labels of the scalars on which the bias will act=dNH1.min
FILE a file in which the list of all deposited kernels is stored=Kernels1.data
TEMP temperature=550
PACEthe frequency for kernel deposition=200
BARRIERthe free energy barrier to be overcome=40
RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=target1
SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD
COMMITTORDoes a committor analysis. More details ...
ARGthe labels of the values which is being used to define the committor surface=dNH1.min
STRIDE the frequency with which the CVs are analyzed=5000
BASIN_LL1List of lower limits for basin #=0.0
BASIN_UL1List of upper limits for basin #=1.1
... COMMITTOR
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=10 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
