Project ID: plumID:22.025
Source: p0.026/t0.8580-recross/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 NATURAL use natural units
The UNITS action with label calculates somethingVOLUMECalculate the volume 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 |
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-17576
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=1.6 D_MAX=2.5}
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=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 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=1.6 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 ---
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=coord.lessthan
STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0 AT0ATx is equal to the position of the restraint at time STEPx=0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=1.0
STEP1This keyword appears multiple times as STEPx with x=0,1,2,=100000 AT1ATx is equal to the position of the restraint at time STEPx=335 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=1.0
STEP2This keyword appears multiple times as STEPx with x=0,1,2,=200000 AT2ATx is equal to the position of the restraint at time STEPx=335 KAPPA2KAPPAx is equal to the value of the force constants at time STEPx=1.0
STRIDEthe frequency with which the forces due to the bias should be calculated=10
LABELa label for the action so that its output can be referenced in the input to other actions=resThe MOVINGRESTRAINT 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 |
| res.coord_lessthan_cntr | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _cntr. These quantities give the instantaneous position of the center of the harmonic potential. This particular component measures this quantity for the input CV named coord_lessthan |
| res.coord_lessthan_work | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _work. These quantities tell the user how much work has been done by the potential in dragging the system along the various colvar axis. This particular component measures this quantity for the input CV named coord_lessthan |
| res.coord_lessthan_kappa | scalar | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _kappa. These quantities tell the user the time dependent value of kappa. This particular component measures this quantity for the input CV named coord_lessthan |
| res.work | scalar | the total work performed changing this restraint |
... MOVINGRESTRAINT
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=coord.lessthan
STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0 AT0ATx is equal to the position of the restraint at time STEPx=0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=1.0
STEP1This keyword appears multiple times as STEPx with x=0,1,2,=100000 AT1ATx is equal to the position of the restraint at time STEPx=335 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=1.0
STEP2This keyword appears multiple times as STEPx with x=0,1,2,=200000 AT2ATx is equal to the position of the restraint at time STEPx=335 KAPPA2KAPPAx is equal to the value of the force constants at time STEPx=1.0
STRIDEthe frequency with which the forces due to the bias should be calculated=10
LABELa label for the action so that its output can be referenced in the input to other actions=res
VERSE Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B)=B
... MOVINGRESTRAINT
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,res.work 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
