Project ID: plumID:21.002
Source: Crystallization/IceIc/64molecules/350K/plumed.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=1-192:3
SIGMA the width to use for the gaussian kernels=0.050
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=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=8 MM=16}
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=1-192:3
SIGMA the width to use for the gaussian kernels=0.050
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=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=8 MM=16}
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=1-192:3 CUTOFF ignore distances that have a value larger than this cutoff=0.608629
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=1-192:3
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=64
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(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y--0.1622)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y-0.1621)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1622)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1621)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3242)^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(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y--0.1621)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y-0.1622)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1621)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1622)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3243)^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
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 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))
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=8 MM=16}
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 ---
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=64.0
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
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
