Project ID: plumID:22.025
Source: p0.026/t0.8580-recross/plumed2.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 NATURAL use natural units
The UNITS action with label calculates somethingVOLUMECalculate the volume of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=volThe VOLUME action with label vol calculates the following quantities:| Quantity | Type | Description |
| vol | scalar | the volume of simulation box |
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=vol FUNCthe function you wish to evaluate=x/17576 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=molvolThe CUSTOM action with label molvol calculates the following quantities:| Quantity | Type | Description |
| molvol | scalar | an arbitrary function |
COORDINATIONNUMBERCalculate 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_lessthan | scalar | the number of colvars that have a value less than a threshold |
SPECIESthis keyword is used for colvars such as coordination number=1-17576
SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=1.6 D_MAX=2.5}
LESS_THANcalculate the number of variables that are less than a certain target value={RATIONAL R_0=5 D_MAX=7.5 NN=12}
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=1-17576
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=1-17576 SWITCHspecify the switching function to use between two sets of indistinguishable atoms={RATIONAL R_0=1.6 D_MAX=2.5}
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=17576
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_ltThe LESS_THAN action with label coord_lt calculates the following quantities:| Quantity | Type | Description |
| coord_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=coord SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=5 D_MAX=7.5 NN=12}
coord_lessthanThe SUM action with label coord_lessthan calculates the following quantities:| Quantity | Type | Description |
| coord_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=coord_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
COMMITTORDoes a committor analysis. More details ...
ARGthe labels of the values which is being used to define the committor surface=coord.lessthan
STRIDE the frequency with which the CVs are analyzed=1
BASIN_LL1List of lower limits for basin #=0
BASIN_UL1List of upper limits for basin #=335
BASIN_LL2List of lower limits for basin #=335
BASIN_UL2List of upper limits for basin #=17576
NOSTOP if true do not stop the simulation when reaching a basin but just keep track of it
FILEthe name of the file on which to output the reached basin=commit
... COMMITTOR
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=2000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=molvol,coord.lessthan STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=colvar
