Project ID: plumID:21.002
Source: Crystallization/IceIh/288molecules/350K/plumed.start.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.
volThe VOLUME action with label vol calculates the following quantities:| Quantity | Type | Description |
| vol | scalar | the volume of simulation box |
: VOLUMECalculate the volume of the simulation box. More details
ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More details ...
SPECIESthis keyword is used for colvars such as coordination number=1-864:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
LABELa label for the action so that its output can be referenced in the input to other actions=refcvThe ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:| Quantity | Type | Description |
| refcv | vector | the environmental similar parameter for each of the input atoms |
| refcv_morethan | scalar | the number of colvars that have a value more than a threshold |
| refcv_mean | scalar | the mean of the colvars |
REFERENCE_1PDB files with relative distances from central atom=env1h.pdb
REFERENCE_2PDB files with relative distances from central atom=env2h.pdb
REFERENCE_3PDB files with relative distances from central atom=env3h.pdb
REFERENCE_4PDB files with relative distances from central atom=env4h.pdb
MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=6 MM=12}
MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and uses the defaults shown here. More details ...
SPECIESthis keyword is used for colvars such as coordination number=1-864:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
LABELa label for the action so that its output can be referenced in the input to other actions=refcv
REFERENCE_1PDB files with relative distances from central atom=env1h.pdb
REFERENCE_2PDB files with relative distances from central atom=env2h.pdb
REFERENCE_3PDB files with relative distances from central atom=env3h.pdb
REFERENCE_4PDB files with relative distances from central atom=env4h.pdb
MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=6 MM=12}
MEAN calculate the mean of all the quantities
CUTOFF how many multiples of sigma would you like to consider beyond the maximum distance in the environment=3 LCUTOFF any atoms separated by less than this tolerance should be ignored=0.0001 LAMBDA Lambda parameter=100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv_cmatThe DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities:| Quantity | Type | Description |
| refcv_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| refcv_cmat.x | matrix | the projection of the bond on the x axis |
| refcv_cmat.y | matrix | the projection of the bond on the y axis |
| refcv_cmat.z | matrix | the projection of the bond on the z axis |
: DISTANCE_MATRIXCalculate a matrix of distances More details COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix GROUPthe atoms for which you would like to calculate the adjacency matrix=1-864:3 CUTOFF ignore distances that have a value larger than this cutoff=0.6085
refcv_grpThe GROUP action with label refcv_grp calculates the following quantities:| Quantity | Type | Description |
| refcv_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=1-864:3
refcv_onesThe CONSTANT action with label refcv_ones calculates the following quantities:| Quantity | Type | Description |
| refcv_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=288
refcv_matenv1The CUSTOM action with label refcv_matenv1 calculates the following quantities:| Quantity | Type | Description |
| refcv_matenv1 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(step(w-0.0001)*step(0.6085-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025)))
refcv_env1The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities:| Quantity | Type | Description |
| refcv_env1 | 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=refcv_matenv1,refcv_ones
refcv_matenv2The CUSTOM action with label refcv_matenv2 calculates the following quantities:| Quantity | Type | Description |
| refcv_matenv2 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(step(w-0.0001)*step(0.6085-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025)))
refcv_env2The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities:| Quantity | Type | Description |
| refcv_env2 | 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=refcv_matenv2,refcv_ones
refcv_matenv3The CUSTOM action with label refcv_matenv3 calculates the following quantities:| Quantity | Type | Description |
| refcv_matenv3 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(step(w-0.0001)*step(0.6085-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025)))
refcv_env3The MATRIX_VECTOR_PRODUCT action with label refcv_env3 calculates the following quantities:| Quantity | Type | Description |
| refcv_env3 | 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=refcv_matenv3,refcv_ones
refcv_matenv4The CUSTOM action with label refcv_matenv4 calculates the following quantities:| Quantity | Type | Description |
| refcv_matenv4 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(step(w-0.0001)*step(0.6085-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.0025)))
refcv_env4The MATRIX_VECTOR_PRODUCT action with label refcv_env4 calculates the following quantities:| Quantity | Type | Description |
| refcv_env4 | 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=refcv_matenv4,refcv_ones
refcvThe CUSTOM action with label refcv calculates the following quantities:| Quantity | Type | Description |
| refcv | 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=refcv_env1,refcv_env2,refcv_env3,refcv_env4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO VARthe names to give each of the arguments in the function=v1,v2,v3,v4 FUNCthe function you wish to evaluate=(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4))
refcv_mtThe MORE_THAN action with label refcv_mt calculates the following quantities:| Quantity | Type | Description |
| refcv_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=refcv SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.5 NN=6 MM=12}
refcv_morethanThe SUM action with label refcv_morethan calculates the following quantities:| Quantity | Type | Description |
| refcv_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=refcv_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
refcv_meanThe MEAN action with label refcv_mean calculates the following quantities:| Quantity | Type | Description |
| refcv_mean | 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=refcv PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
energyThe ENERGY action with label energy calculates the following quantities:| Quantity | Type | Description |
| energy | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
bf1: BF_LEGENDRELegendre polynomials basis functions. More details ORDERThe order of the basis function expansion=40 MINIMUMThe minimum of the interval on which the basis functions are defined=0.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=288.0
The BF_LEGENDRE action with label bf1 calculates somethingtd_uni: TD_UNIFORMUniform target distribution (static). More details
The TD_UNIFORM action with label td_uni calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. More details ...
ARGthe labels of the scalars on which the bias will act=refcv.morethan
BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=350.0
GRID_BINSthe number of bins used for the grid=300
TARGET_DISTRIBUTIONthe label of the target distribution to be used=td_uni
LABELa label for the action so that its output can be referenced in the input to other actions=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities:| Quantity | Type | Description |
| b1.bias | scalar | the instantaneous value of the bias potential |
| b1.force2 | scalar | the instantaneous value of the squared force due to this bias potential. |
... VES_LINEAR_EXPANSION
OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action has hidden defaults. More details ...
BIASthe label of the VES bias to be optimized=b1
STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
LABELa label for the action so that its output can be referenced in the input to other actions=o1
STEPSIZEthe step size used for the optimization=1
FES_OUTPUThow often the FES(s) should be written out to file=500
BIAS_OUTPUThow often the bias(es) should be written out to file=500
COEFFS_OUTPUT how often the coefficients should be written to file=100
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:| Quantity | Description |
| o1.value | a scalar |
OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More details ...
BIASthe label of the VES bias to be optimized=b1
STRIDEthe frequency of updating the coefficients given in the number of MD steps=500
LABELa label for the action so that its output can be referenced in the input to other actions=o1
STEPSIZEthe step size used for the optimization=1
FES_OUTPUThow often the FES(s) should be written out to file=500
BIAS_OUTPUThow often the bias(es) should be written out to file=500
COEFFS_OUTPUT how often the coefficients should be written to file=100
COEFFS_FILE the name of output file for the coefficients=coeffs.data
... OPT_AVERAGED_SGD
ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and it has hidden defaults. More details ...
SPECIESthis keyword is used for colvars such as coordination number=1-864:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
LABELa label for the action so that its output can be referenced in the input to other actions=refcv2The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities:| Quantity | Type | Description |
| refcv2 | vector | the environmental similar parameter for each of the input atoms |
| refcv2_morethan | scalar | the number of colvars that have a value more than a threshold |
| refcv2_mean | scalar | the mean of the colvars |
REFERENCE_1PDB files with relative distances from central atom=env1c.pdb
REFERENCE_2PDB files with relative distances from central atom=env2c.pdb
MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=6 MM=12}
MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. This action is a shortcut and uses the defaults shown here. More details ...
SPECIESthis keyword is used for colvars such as coordination number=1-864:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
LABELa label for the action so that its output can be referenced in the input to other actions=refcv2
REFERENCE_1PDB files with relative distances from central atom=env1c.pdb
REFERENCE_2PDB files with relative distances from central atom=env2c.pdb
MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=6 MM=12}
MEAN calculate the mean of all the quantities
CUTOFF how many multiples of sigma would you like to consider beyond the maximum distance in the environment=3 LCUTOFF any atoms separated by less than this tolerance should be ignored=0.0001 LAMBDA Lambda parameter=100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv2_cmatThe DISTANCE_MATRIX action with label refcv2_cmat calculates the following quantities:| Quantity | Type | Description |
| refcv2_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| refcv2_cmat.x | matrix | the projection of the bond on the x axis |
| refcv2_cmat.y | matrix | the projection of the bond on the y axis |
| refcv2_cmat.z | matrix | the projection of the bond on the z axis |
: DISTANCE_MATRIXCalculate a matrix of distances More details COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix GROUPthe atoms for which you would like to calculate the adjacency matrix=1-864:3 CUTOFF ignore distances that have a value larger than this cutoff=0.608694
refcv2_grpThe GROUP action with label refcv2_grp calculates the following quantities:| Quantity | Type | Description |
| refcv2_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=1-864:3
refcv2_onesThe CONSTANT action with label refcv2_ones calculates the following quantities:| Quantity | Type | Description |
| refcv2_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=288
refcv2_matenv1The CUSTOM action with label refcv2_matenv1 calculates the following quantities:| Quantity | Type | Description |
| refcv2_matenv1 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(step(w-0.0001)*step(0.608694-w)/16)*(exp(-((x--0.4585)^2+(y--0.0001)^2+(z-0.0019)^2)/(4*0.0025))+exp(-((x--0.2307)^2+(y--0.1316)^2+(z--0.3738)^2)/(4*0.0025))+exp(-((x--0.2296)^2+(y--0.1323)^2+(z--0.093)^2)/(4*0.0025))+exp(-((x--0.2293)^2+(y--0.3972)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.2292)^2+(y-0.397)^2+(z-0.0018)^2)/(4*0.0025))+exp(-((x--0.2278)^2+(y-0.1314)^2+(z-0.3756)^2)/(4*0.0025))+exp(-((x--0.0015)^2+(y-0.2655)^2+(z--0.3737)^2)/(4*0.0025))+exp(-((x--0.0003)^2+(y-0.2649)^2+(z--0.093)^2)/(4*0.0025))+exp(-((x-0.0012)^2+(y--0.0008)^2+(z-0.2809)^2)/(4*0.0025))+exp(-((x-0.0015)^2+(y--0.2657)^2+(z-0.3739)^2)/(4*0.0025))+exp(-((x-0.2278)^2+(y--0.1316)^2+(z--0.3756)^2)/(4*0.0025))+exp(-((x-0.229)^2+(y--0.1323)^2+(z--0.0948)^2)/(4*0.0025))+exp(-((x-0.2293)^2+(y-0.397)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.2294)^2+(y--0.3972)^2+(z--0.0018)^2)/(4*0.0025))+exp(-((x-0.2309)^2+(y-0.1314)^2+(z-0.3738)^2)/(4*0.0025))+exp(-((x-0.4586)^2+(y--0.0001)^2+(z--0.0018)^2)/(4*0.0025)))
refcv2_env1The MATRIX_VECTOR_PRODUCT action with label refcv2_env1 calculates the following quantities:| Quantity | Type | Description |
| refcv2_env1 | 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=refcv2_matenv1,refcv2_ones
refcv2_matenv2The CUSTOM action with label refcv2_matenv2 calculates the following quantities:| Quantity | Type | Description |
| refcv2_matenv2 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w VARthe names to give each of the arguments in the function=x,y,z,w PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(step(w-0.0001)*step(0.608694-w)/16)*(exp(-((x--0.4586)^2+(y-0.0001)^2+(z-0.0018)^2)/(4*0.0025))+exp(-((x--0.2308)^2+(y--0.1315)^2+(z--0.3739)^2)/(4*0.0025))+exp(-((x--0.2293)^2+(y--0.3971)^2+(z--0.0001)^2)/(4*0.0025))+exp(-((x--0.2293)^2+(y-0.3971)^2+(z-0.0018)^2)/(4*0.0025))+exp(-((x--0.229)^2+(y-0.1322)^2+(z-0.0947)^2)/(4*0.0025))+exp(-((x--0.2278)^2+(y-0.1315)^2+(z-0.3756)^2)/(4*0.0025))+exp(-((x--0.0015)^2+(y-0.2657)^2+(z--0.3739)^2)/(4*0.0025))+exp(-((x--0.0012)^2+(y-0.0008)^2+(z--0.2809)^2)/(4*0.0025))+exp(-((x-0.0003)^2+(y--0.2649)^2+(z-0.093)^2)/(4*0.0025))+exp(-((x-0.0015)^2+(y--0.2655)^2+(z-0.3737)^2)/(4*0.0025))+exp(-((x-0.2278)^2+(y--0.1315)^2+(z--0.3757)^2)/(4*0.0025))+exp(-((x-0.2292)^2+(y--0.3971)^2+(z--0.0019)^2)/(4*0.0025))+exp(-((x-0.2293)^2+(y-0.3971)^2+(z--0.0001)^2)/(4*0.0025))+exp(-((x-0.2297)^2+(y-0.1322)^2+(z-0.0929)^2)/(4*0.0025))+exp(-((x-0.2307)^2+(y-0.1315)^2+(z-0.3737)^2)/(4*0.0025))+exp(-((x-0.4585)^2+(y-0.0001)^2+(z--0.0019)^2)/(4*0.0025)))
refcv2_env2The MATRIX_VECTOR_PRODUCT action with label refcv2_env2 calculates the following quantities:| Quantity | Type | Description |
| refcv2_env2 | 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=refcv2_matenv2,refcv2_ones
refcv2The CUSTOM action with label refcv2 calculates the following quantities:| Quantity | Type | Description |
| refcv2 | 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=refcv2_env1,refcv2_env2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO VARthe names to give each of the arguments in the function=v1,v2 FUNCthe function you wish to evaluate=(1/100)*log(exp(100*v1)+exp(100*v2))
refcv2_mtThe MORE_THAN action with label refcv2_mt calculates the following quantities:| Quantity | Type | Description |
| refcv2_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=refcv2 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.5 NN=6 MM=12}
refcv2_morethanThe SUM action with label refcv2_morethan calculates the following quantities:| Quantity | Type | Description |
| refcv2_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=refcv2_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
refcv2_meanThe MEAN action with label refcv2_mean calculates the following quantities:| Quantity | Type | Description |
| refcv2_mean | 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=refcv2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
diffThe MATHEVAL action with label diff calculates the following quantities:| Quantity | Type | Description |
| diff | scalar | an arbitrary function |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=refcv2.mean,refcv.mean FUNCthe function you wish to evaluate=((x-0.2075)/(0.5821-0.2075)-(y-0.2319)/(0.8137-0.2319)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=100000 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 |
Q6Calculate sixth order Steinhardt parameters. This action is a shortcut. More details SPECIESthis keyword is used for colvars such as coordination number=1-864:3 SWITCHthe switching function that it used in the construction of the contact matrix={CUBIC D_0=0.3 D_MAX=0.35} VMEAN calculate the norm of the mean vector LABELa label for the action so that its output can be referenced in the input to other actions=q6The Q6 action with label q6 calculates the following quantities:| Quantity | Type | Description |
| q6 | vector | the norms of the vectors of spherical harmonic coefficients |
# Q6 SPECIES=1-864:3 SWITCH={CUBIC D_0=0.3 D_MAX=0.35} VMEAN LABEL=q6
q6_grpThe GROUP action with label q6_grp calculates the following quantities:| Quantity | Type | Description |
| q6_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=1-864:3
q6_matThe CONTACT_MATRIX action with label q6_mat calculates the following quantities:| Quantity | Type | Description |
| q6_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| q6_mat.x | matrix | the projection of the bond on the x axis |
| q6_mat.y | matrix | the projection of the bond on the y axis |
| q6_mat.z | matrix | the projection of the bond on the z axis |
: 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=1-864:3 SWITCHspecify the switching function to use between two sets of indistinguishable atoms={CUBIC D_0=0.3 D_MAX=0.35} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix
q6_shThe SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities:| Quantity | Type | Description |
| q6_sh.rm-n6 | matrix | the real parts of the spherical harmonic values with the m value given This is the n6th of these quantities |
| q6_sh.rm-n5 | matrix | the real parts of the spherical harmonic values with the m value given This is the n5th of these quantities |
| q6_sh.rm-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q6_sh.rm-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q6_sh.rm-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q6_sh.rm-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q6_sh.rm-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q6_sh.rm-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q6_sh.rm-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q6_sh.rm-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q6_sh.rm-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
| q6_sh.rm-p5 | matrix | the real parts of the spherical harmonic values with the m value given This is the p5th of these quantities |
| q6_sh.rm-p6 | matrix | the real parts of the spherical harmonic values with the m value given This is the p6th of these quantities |
| q6_sh.im-n6 | matrix | the real parts of the spherical harmonic values with the m value given This is the n6th of these quantities |
| q6_sh.im-n5 | matrix | the real parts of the spherical harmonic values with the m value given This is the n5th of these quantities |
| q6_sh.im-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q6_sh.im-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q6_sh.im-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q6_sh.im-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q6_sh.im-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q6_sh.im-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q6_sh.im-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q6_sh.im-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q6_sh.im-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
| q6_sh.im-p5 | matrix | the real parts of the spherical harmonic values with the m value given This is the p5th of these quantities |
| q6_sh.im-p6 | matrix | the real parts of the spherical harmonic values with the m value given This is the p6th of these quantities |
: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q6_mat.x,q6_mat.y,q6_mat.z,q6_mat.w Lthe value of the angular momentum=6
q6_denom_onesThe CONSTANT action with label q6_denom_ones calculates the following quantities:| Quantity | Type | Description |
| q6_denom_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=288
q6_denomThe MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities:| Quantity | Type | Description |
| q6_denom | 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=q6_mat.w,q6_denom_ones
q6_spThe MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities:| Quantity | Type | Description |
| q6_sp.rm-n6 | vector | the product of the matrix q6_sh.rm-n6 and the vector q6_denom_ones |
| q6_sp.rm-n5 | vector | the product of the matrix q6_sh.rm-n5 and the vector q6_denom_ones |
| q6_sp.rm-n4 | vector | the product of the matrix q6_sh.rm-n4 and the vector q6_denom_ones |
| q6_sp.rm-n3 | vector | the product of the matrix q6_sh.rm-n3 and the vector q6_denom_ones |
| q6_sp.rm-n2 | vector | the product of the matrix q6_sh.rm-n2 and the vector q6_denom_ones |
| q6_sp.rm-n1 | vector | the product of the matrix q6_sh.rm-n1 and the vector q6_denom_ones |
| q6_sp.rm-0 | vector | the product of the matrix q6_sh.rm-0 and the vector q6_denom_ones |
| q6_sp.rm-p1 | vector | the product of the matrix q6_sh.rm-p1 and the vector q6_denom_ones |
| q6_sp.rm-p2 | vector | the product of the matrix q6_sh.rm-p2 and the vector q6_denom_ones |
| q6_sp.rm-p3 | vector | the product of the matrix q6_sh.rm-p3 and the vector q6_denom_ones |
| q6_sp.rm-p4 | vector | the product of the matrix q6_sh.rm-p4 and the vector q6_denom_ones |
| q6_sp.rm-p5 | vector | the product of the matrix q6_sh.rm-p5 and the vector q6_denom_ones |
| q6_sp.rm-p6 | vector | the product of the matrix q6_sh.rm-p6 and the vector q6_denom_ones |
| q6_sp.im-n6 | vector | the product of the matrix q6_sh.im-n6 and the vector q6_denom_ones |
| q6_sp.im-n5 | vector | the product of the matrix q6_sh.im-n5 and the vector q6_denom_ones |
| q6_sp.im-n4 | vector | the product of the matrix q6_sh.im-n4 and the vector q6_denom_ones |
| q6_sp.im-n3 | vector | the product of the matrix q6_sh.im-n3 and the vector q6_denom_ones |
| q6_sp.im-n2 | vector | the product of the matrix q6_sh.im-n2 and the vector q6_denom_ones |
| q6_sp.im-n1 | vector | the product of the matrix q6_sh.im-n1 and the vector q6_denom_ones |
| q6_sp.im-0 | vector | the product of the matrix q6_sh.im-0 and the vector q6_denom_ones |
| q6_sp.im-p1 | vector | the product of the matrix q6_sh.im-p1 and the vector q6_denom_ones |
| q6_sp.im-p2 | vector | the product of the matrix q6_sh.im-p2 and the vector q6_denom_ones |
| q6_sp.im-p3 | vector | the product of the matrix q6_sh.im-p3 and the vector q6_denom_ones |
| q6_sp.im-p4 | vector | the product of the matrix q6_sh.im-p4 and the vector q6_denom_ones |
| q6_sp.im-p5 | vector | the product of the matrix q6_sh.im-p5 and the vector q6_denom_ones |
| q6_sp.im-p6 | vector | the product of the matrix q6_sh.im-p6 and the vector q6_denom_ones |
: 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=q6_sh.*,q6_denom_ones
q6_rmn-n6The CUSTOM action with label q6_rmn-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n6 | 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=q6_sp.rm-n6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n6The CUSTOM action with label q6_imn-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n6 | 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=q6_sp.im-n6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n5The CUSTOM action with label q6_rmn-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n5 | 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=q6_sp.rm-n5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n5The CUSTOM action with label q6_imn-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n5 | 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=q6_sp.im-n5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n4The CUSTOM action with label q6_rmn-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n4 | 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=q6_sp.rm-n4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n4The CUSTOM action with label q6_imn-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n4 | 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=q6_sp.im-n4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n3The CUSTOM action with label q6_rmn-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n3 | 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=q6_sp.rm-n3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n3The CUSTOM action with label q6_imn-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n3 | 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=q6_sp.im-n3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n2The CUSTOM action with label q6_rmn-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n2 | 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=q6_sp.rm-n2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n2The CUSTOM action with label q6_imn-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n2 | 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=q6_sp.im-n2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-n1The CUSTOM action with label q6_rmn-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-n1 | 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=q6_sp.rm-n1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-n1The CUSTOM action with label q6_imn-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-n1 | 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=q6_sp.im-n1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-0The CUSTOM action with label q6_rmn-0 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-0 | 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=q6_sp.rm-0,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-0The CUSTOM action with label q6_imn-0 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-0 | 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=q6_sp.im-0,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p1The CUSTOM action with label q6_rmn-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p1 | 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=q6_sp.rm-p1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p1The CUSTOM action with label q6_imn-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p1 | 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=q6_sp.im-p1,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p2The CUSTOM action with label q6_rmn-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p2 | 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=q6_sp.rm-p2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p2The CUSTOM action with label q6_imn-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p2 | 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=q6_sp.im-p2,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p3The CUSTOM action with label q6_rmn-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p3 | 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=q6_sp.rm-p3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p3The CUSTOM action with label q6_imn-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p3 | 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=q6_sp.im-p3,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p4The CUSTOM action with label q6_rmn-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p4 | 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=q6_sp.rm-p4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p4The CUSTOM action with label q6_imn-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p4 | 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=q6_sp.im-p4,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p5The CUSTOM action with label q6_rmn-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p5 | 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=q6_sp.rm-p5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p5The CUSTOM action with label q6_imn-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p5 | 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=q6_sp.im-p5,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rmn-p6The CUSTOM action with label q6_rmn-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_rmn-p6 | 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=q6_sp.rm-p6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_imn-p6The CUSTOM action with label q6_imn-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_imn-p6 | 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=q6_sp.im-p6,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n6The MEAN action with label q6_rms-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n6 | 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=q6_rmn-n6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n6The MEAN action with label q6_ims-n6 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n6 | 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=q6_imn-n6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n5The MEAN action with label q6_rms-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n5 | 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=q6_rmn-n5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n5The MEAN action with label q6_ims-n5 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n5 | 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=q6_imn-n5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n4The MEAN action with label q6_rms-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n4 | 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=q6_rmn-n4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n4The MEAN action with label q6_ims-n4 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n4 | 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=q6_imn-n4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n3The MEAN action with label q6_rms-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n3 | 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=q6_rmn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n3The MEAN action with label q6_ims-n3 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n3 | 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=q6_imn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n2The MEAN action with label q6_rms-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n2 | 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=q6_rmn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n2The MEAN action with label q6_ims-n2 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n2 | 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=q6_imn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-n1The MEAN action with label q6_rms-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-n1 | 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=q6_rmn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-n1The MEAN action with label q6_ims-n1 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-n1 | 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=q6_imn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-0The MEAN action with label q6_rms-0 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-0 | 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=q6_rmn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-0The MEAN action with label q6_ims-0 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-0 | 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=q6_imn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p1The MEAN action with label q6_rms-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p1 | 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=q6_rmn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p1The MEAN action with label q6_ims-p1 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p1 | 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=q6_imn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p2The MEAN action with label q6_rms-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p2 | 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=q6_rmn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p2The MEAN action with label q6_ims-p2 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p2 | 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=q6_imn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p3The MEAN action with label q6_rms-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p3 | 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=q6_rmn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p3The MEAN action with label q6_ims-p3 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p3 | 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=q6_imn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p4The MEAN action with label q6_rms-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p4 | 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=q6_rmn-p4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p4The MEAN action with label q6_ims-p4 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p4 | 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=q6_imn-p4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p5The MEAN action with label q6_rms-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p5 | 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=q6_rmn-p5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p5The MEAN action with label q6_ims-p5 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p5 | 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=q6_imn-p5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_rms-p6The MEAN action with label q6_rms-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_rms-p6 | 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=q6_rmn-p6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_ims-p6The MEAN action with label q6_ims-p6 calculates the following quantities:| Quantity | Type | Description |
| q6_ims-p6 | 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=q6_imn-p6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_vmean2The COMBINE action with label q6_vmean2 calculates the following quantities:| Quantity | Type | Description |
| q6_vmean2 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q6_rms-n6,q6_ims-n6,q6_rms-n5,q6_ims-n5,q6_rms-n4,q6_ims-n4,q6_rms-n3,q6_ims-n3,q6_rms-n2,q6_ims-n2,q6_rms-n1,q6_ims-n1,q6_rms-0,q6_ims-0,q6_rms-p1,q6_ims-p1,q6_rms-p2,q6_ims-p2,q6_rms-p3,q6_ims-p3,q6_rms-p4,q6_ims-p4,q6_rms-p5,q6_ims-p5,q6_rms-p6,q6_ims-p6
q6_vmeanThe CUSTOM action with label q6_vmean calculates the following quantities:| Quantity | Type | Description |
| q6_vmean | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q6_vmean2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6_norm2The COMBINE action with label q6_norm2 calculates the following quantities:| Quantity | Type | Description |
| q6_norm2 | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO POWERS the powers to which you are raising each of the arguments in your function=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q6_sp.rm-n6,q6_sp.im-n6,q6_sp.rm-n5,q6_sp.im-n5,q6_sp.rm-n4,q6_sp.im-n4,q6_sp.rm-n3,q6_sp.im-n3,q6_sp.rm-n2,q6_sp.im-n2,q6_sp.rm-n1,q6_sp.im-n1,q6_sp.rm-0,q6_sp.im-0,q6_sp.rm-p1,q6_sp.im-p1,q6_sp.rm-p2,q6_sp.im-p2,q6_sp.rm-p3,q6_sp.im-p3,q6_sp.rm-p4,q6_sp.im-p4,q6_sp.rm-p5,q6_sp.im-p5,q6_sp.rm-p6,q6_sp.im-p6
q6_normThe CUSTOM action with label q6_norm calculates the following quantities:| Quantity | Type | Description |
| q6_norm | 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=q6_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
q6The CUSTOM action with label q6 calculates the following quantities:| Quantity | Type | Description |
| q6 | 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=q6_norm,q6_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- diff2The MATHEVAL action with label diff2 calculates the following quantities:| Quantity | Type | Description |
| diff2 | scalar | an arbitrary function |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=q6.vmean,refcv.mean FUNCthe function you wish to evaluate=((x-0.0402)/(0.4404-0.0402)-(y-0.2319)/(0.8137-0.2319)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=diff2 ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=100000 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=uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:| Quantity | Type | Description |
| uwall2.bias | scalar | the instantaneous value of the bias potential |
| uwall2.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 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
