Project ID: plumID:24.006
Source: chemicalPotentialDifference/plumed.dat
Originally used with PLUMED version: 2.8
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=ps ENERGYthe units of energy=eV
The UNITS action with label calculates somethingc1The COORDINATIONNUMBER action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | vector | the coordination numbers of the specified atoms |
| c1_lessthan | scalar | the number of colvars that have a value less than a threshold |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-3000:3 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 R_0=1 D_0=3.5 D_MAX=4.5} LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=2 NN=12 MM=24} LOWMEM this flag does nothing and is present only to ensure back-compatibility
# c1: COORDINATIONNUMBER SPECIES=1-3000:3 SWITCH={RATIONAL R_0=1 D_0=3.5 D_MAX=4.5} LESS_THAN={RATIONAL R_0=2 NN=12 MM=24} LOWMEM
c1_grpThe GROUP action with label c1_grp calculates the following quantities:| Quantity | Type | Description |
| c1_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=1-3000:3
c1_matThe CONTACT_MATRIX action with label c1_mat calculates the following quantities:| Quantity | Type | Description |
| c1_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-3000:3 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 R_0=1 D_0=3.5 D_MAX=4.5}
c1_onesThe CONSTANT action with label c1_ones calculates the following quantities:| Quantity | Type | Description |
| c1_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=1000
c1The MATRIX_VECTOR_PRODUCT action with label c1 calculates the following quantities:| Quantity | Type | Description |
| c1 | 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=c1_mat,c1_ones
c1_caverageThe MEAN action with label c1_caverage calculates the following quantities:| Quantity | Type | Description |
| c1_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=c1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c1_ltThe LESS_THAN action with label c1_lt calculates the following quantities:| Quantity | Type | Description |
| c1_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=c1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=2 NN=12 MM=24}
c1_lessthanThe SUM action with label c1_lessthan calculates the following quantities:| Quantity | Type | Description |
| c1_lessthan | 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=c1_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- mtThe METAD action with label mt calculates the following quantities:| Quantity | Type | Description |
| mt.bias | scalar | the instantaneous value of the bias potential |
| mt.rbias | scalar | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram. |
| mt.rct | scalar | the reweighting factor c(t). |
: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=c1.lessthan ...
PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=0.02 BIASFACTORuse well tempered metadynamics and use this bias factor=50
SIGMAthe widths of the Gaussian hills=1 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=373
FILE a file in which the list of added hills is stored=HILLS GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=50 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=c1.lessthan ATthe positions of the wall=30.0 KAPPAthe force constant for the wall=0.1 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:| Quantity | Type | Description |
| uwall.bias | scalar | the instantaneous value of the bias potential |
| uwall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=100
