Project ID: plumID:21.020
Source: droplet/smd/plumed1.inp
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label calculates somethingCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=coordThe COORDINATIONNUMBER action with label coord calculates the following quantities:| Quantity | Type | Description |
| coord | vector | the coordination numbers of the specified atoms |
| coord_morethan | scalar | the number of colvars that have a value more than a threshold |
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-512
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=5.0 D_MAX=10.0}
MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=5.0 D_MAX=5.5}
LOWMEM this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER
# COORDINATIONNUMBER ...
coord_grpThe GROUP action with label coord_grp calculates the following quantities:| Quantity | Type | Description |
| coord_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=1-512
coord_matThe CONTACT_MATRIX action with label coord_mat calculates the following quantities:| Quantity | Type | Description |
| coord_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=1-512 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=5.0 D_MAX=10.0}
coord_onesThe CONSTANT action with label coord_ones calculates the following quantities:| Quantity | Type | Description |
| coord_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=512
coordThe MATRIX_VECTOR_PRODUCT action with label coord calculates the following quantities:| Quantity | Type | Description |
| coord | 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=coord_mat,coord_ones
coord_caverageThe MEAN action with label coord_caverage calculates the following quantities:| Quantity | Type | Description |
| coord_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=coord PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
coord_mtThe MORE_THAN action with label coord_mt calculates the following quantities:| Quantity | Type | Description |
| coord_mt | vector | the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors |
: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=coord SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=5.0 D_MAX=5.5}
coord_morethanThe SUM action with label coord_morethan calculates the following quantities:| Quantity | Type | Description |
| coord_morethan | 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=coord_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=coord.morethan ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=1.0 LABELa label for the action so that its output can be referenced in the input to other actions=resThe RESTRAINT action with label res calculates the following quantities:| Quantity | Type | Description |
| res.bias | scalar | the instantaneous value of the bias potential |
| res.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=coord.morethan ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=1.0 LABELa label for the action so that its output can be referenced in the input to other actions=res SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
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=200000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=coord.morethan STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=colvar
