Project ID: plumID:22.008
Source: LJ-cluster/plumed.dat
Originally used with PLUMED version: 2.7
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 TIMEthe units of time=0.0101805 ENERGYthe units of energy=96.4853329
The UNITS action with label calculates somethingUNITSThis command sets the internal units for the code. More details NATURAL use natural units
COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-7 LABELa label for the action so that its output can be referenced in the input to other actions=comThe COM action with label com calculates the following quantities: Quantity | Type | Description |
com | atoms | virtual atom calculated by COM action |
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,com LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities: Quantity | Type | Description |
d1 | scalar | the DISTANCE between this pair of atoms |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=100.
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,com LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCE action with label d2 calculates the following quantities: Quantity | Type | Description |
d2 | scalar | the DISTANCE between this pair of atoms |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d2 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=100.
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,com LABELa label for the action so that its output can be referenced in the input to other actions=d3The DISTANCE action with label d3 calculates the following quantities: Quantity | Type | Description |
d3 | scalar | the DISTANCE between this pair of atoms |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d3 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=100.
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,com LABELa label for the action so that its output can be referenced in the input to other actions=d4The DISTANCE action with label d4 calculates the following quantities: Quantity | Type | Description |
d4 | scalar | the DISTANCE between this pair of atoms |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d4 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=100.
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,com LABELa label for the action so that its output can be referenced in the input to other actions=d5The DISTANCE action with label d5 calculates the following quantities: Quantity | Type | Description |
d5 | scalar | the DISTANCE between this pair of atoms |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d5 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=100.
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,com LABELa label for the action so that its output can be referenced in the input to other actions=d6The DISTANCE action with label d6 calculates the following quantities: Quantity | Type | Description |
d6 | scalar | the DISTANCE between this pair of atoms |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d6 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=100.
DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,com LABELa label for the action so that its output can be referenced in the input to other actions=d7The DISTANCE action with label d7 calculates the following quantities: Quantity | Type | Description |
d7 | scalar | the DISTANCE between this pair of atoms |
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d7 ATthe positions of the wall=2.0 KAPPAthe force constant for the wall=100.
c1The COORDINATIONNUMBER action with label c1 calculates the following quantities: Quantity | Type | Description |
c1 | vector | the coordination numbers of the specified atoms |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthis keyword is used for colvars such as coordination number=1-7 MOMENTSthe list of moments that you would like to calculate=2-3 SWITCHthe switching function that it used in the construction of the contact matrix={RATIONAL R_0=1.5 NN=8 MM=16}
# c1: COORDINATIONNUMBER SPECIES=1-7 MOMENTS=2-3 SWITCH={RATIONAL R_0=1.5 NN=8 MM=16}
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=1-7
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=1-7 SWITCHspecify the switching function to use between two sets of indistinguishable atoms={RATIONAL R_0=1.5 NN=8 MM=16}
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=7
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_diffpow-2The CUSTOM action with label c1_diffpow-2 calculates the following quantities: Quantity | Type | Description |
c1_diffpow-2 | 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=c1,c1_caverage PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(x-y)^2
c1_moment-2The MEAN action with label c1_moment-2 calculates the following quantities: Quantity | Type | Description |
c1_moment-2 | 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_diffpow-2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
c1_diffpow-3The CUSTOM action with label c1_diffpow-3 calculates the following quantities: Quantity | Type | Description |
c1_diffpow-3 | 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=c1,c1_caverage PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(x-y)^3
c1_moment-3The MEAN action with label c1_moment-3 calculates the following quantities: Quantity | Type | Description |
c1_moment-3 | 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_diffpow-3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=c1.* HEIGHTthe heights of the Gaussian hills=0.05 PACEthe frequency for hill addition=500 SIGMAthe widths of the Gaussian hills=0.1,0.1 GRID_MINthe lower bounds for the grid=-1.5,-1.5 GRID_MAXthe upper bounds for the grid=2.5,2.5 GRID_BINthe number of bins for the grid=500,500 BIASFACTORuse well tempered metadynamics and use this bias factor=5 FILE a file in which the list of added hills is stored=HILLS