PLUMED-NEST by plumed-nest

Project ID: plumID:22.016
Source: SurfaceFreeEnergy/Basal/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. 

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=1-1728:3
 SIGMA the width to use for the gaussian kernels=0.0675
 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. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.60 D_MAX=0.98}
 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=1-1728:3
 SIGMA the width to use for the gaussian kernels=0.0675
 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. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.60 D_MAX=0.98}
 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
# PLUMED interprets the command:
# ENVIRONMENTSIMILARITY ...
#  SPECIES=1-1728:3
#  SIGMA=0.0675
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv
#  REFERENCE_1=env1h.pdb
#  REFERENCE_2=env2h.pdb
#  REFERENCE_3=env3h.pdb
#  REFERENCE_4=env4h.pdb
#  MORE_THAN={CUBIC D_0=0.60 D_MAX=0.98}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
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 between atoms. More details COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix GROUPthe atoms for which you would like to calculate the adjacency matrix=1-1728:3 CUTOFF ignore distances that have a value larger than this cutoff=0.477631
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=1-1728:3
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=576
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(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625)))
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(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625)))
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(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625)))
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(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625)))
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={CUBIC D_0=0.60 D_MAX=0.98}
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 --- 
sThe AROUND action with label s calculates the following quantities: Quantity    Type    Description  
s_mean scalar the average values of the colvar in the region of interest
s_morethan scalar the number of cvs in the region of interest that are more than a certain threshold: AROUNDThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. This action is a shortcut. More details DATAthe label of an action that calculates multicolvars=refcv ATOMan alternative to ORIGIN=1 ZLOWER the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)=-0.5 ZUPPER the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)=0.5 SIGMAthe width of the function to be used for kernel density estimation=0.03 MEAN calculate the average value of the colvar inside the region of interest MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={CUBIC D_0=0.60 D_MAX=0.98}
# PLUMED interprets the command:
# s: AROUND DATA=refcv ATOM=1 ZLOWER=-0.5 ZUPPER=0.5 SIGMA=0.03 MEAN MORE_THAN={CUBIC D_0=0.60 D_MAX=0.98}
# as follows (Click the red comment above to revert to the short version of the input):
s_grpThe GROUP action with label s_grp calculates the following quantities: Quantity    Type    Description  
s_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=refcv
s_prodThe CUSTOM action with label s_prod calculates the following quantities: Quantity    Type    Description  
s_prod 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,s 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
s_numerThe SUM action with label s_numer calculates the following quantities: Quantity    Type    Description  
s_numer 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=s_prod PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
s_normThe SUM action with label s_norm calculates the following quantities: Quantity    Type    Description  
s_norm 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=s PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
s_meanThe CUSTOM action with label s_mean calculates the following quantities: Quantity    Type    Description  
s_mean scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=s_numer,s_norm 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
refcv_s_mtThe MORE_THAN action with label refcv_s_mt calculates the following quantities: Quantity    Type    Description  
refcv_s_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={CUBIC D_0=0.60 D_MAX=0.98}
s_mtThe CUSTOM action with label s_mt calculates the following quantities: Quantity    Type    Description  
s_mt 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_s_mt,s 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
s_morethanThe SUM action with label s_morethan calculates the following quantities: Quantity    Type    Description  
s_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=s_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
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 ...
 SPECIESAthis keyword is used for colvars such as the coordination number=1
 SPECIESBthis keyword is used for colvars such as the coordination number=4-1728:3
 SIGMA the width to use for the gaussian kernels=0.0675
 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=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. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.60 D_MAX=0.98}
 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 ...
 SPECIESAthis keyword is used for colvars such as the coordination number=1
 SPECIESBthis keyword is used for colvars such as the coordination number=4-1728:3
 SIGMA the width to use for the gaussian kernels=0.0675
 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=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. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.60 D_MAX=0.98}
 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
# PLUMED interprets the command:
# ENVIRONMENTSIMILARITY ...
#  SPECIESA=1
#  SPECIESB=4-1728:3
#  SIGMA=0.0675
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv2
#  REFERENCE_1=env1h.pdb
#  REFERENCE_2=env2h.pdb
#  REFERENCE_3=env3h.pdb
#  REFERENCE_4=env4h.pdb
#  MORE_THAN={CUBIC D_0=0.60 D_MAX=0.98}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
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 between atoms. More details COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=4-1728:3 CUTOFF ignore distances that have a value larger than this cutoff=0.477631
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
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=575
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(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625)))
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(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625)))
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
refcv2_matenv3The CUSTOM action with label refcv2_matenv3 calculates the following quantities: Quantity    Type    Description  
refcv2_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=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(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625)))
refcv2_env3The MATRIX_VECTOR_PRODUCT action with label refcv2_env3 calculates the following quantities: Quantity    Type    Description  
refcv2_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=refcv2_matenv3,refcv2_ones
refcv2_matenv4The CUSTOM action with label refcv2_matenv4 calculates the following quantities: Quantity    Type    Description  
refcv2_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=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(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625)))
refcv2_env4The MATRIX_VECTOR_PRODUCT action with label refcv2_env4 calculates the following quantities: Quantity    Type    Description  
refcv2_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=refcv2_matenv4,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,refcv2_env3,refcv2_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))
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={CUBIC D_0=0.60 D_MAX=0.98}
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 --- 
eneThe ENERGY action with label ene calculates the following quantities: Quantity    Type    Description  
ene scalar the internal energy: ENERGYCalculate the total potential energy of the simulation box. 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 the simulation box. More details

OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ARGthe labels of the scalars on which the bias will act=s.morethan,refcv2.morethan PACEthe frequency for kernel deposition=500 STRIDEthe frequency with which the forces due to the bias should be calculated=2 TEMP temperature=312 BARRIERthe free energy barrier to be overcome=350 WALKERS_MPI switch on MPI version of multiple walkers 

The OPES_METAD action with label  calculates the following quantities: Quantity    Description  
.bias the instantaneous value of the bias potential
.rct estimate of c(t)
.zed estimate of Z_n
.neff effective sample size
.nker total number of compressed kernels used to represent the biasENVIRONMENTSIMILARITYMeasure 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=1-1728:3
 SIGMA the width to use for the gaussian kernels=0.08
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv3The ENVIRONMENTSIMILARITY action with label refcv3 calculates the following quantities: Quantity    Type    Description  
refcv3 vector the environmental similar parameter for each of the input atoms
refcv3_morethan scalar the number of colvars that have a value more than a threshold
refcv3_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
 REFERENCE_3PDB files with relative distances from central atom=env3c.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4c.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=1.00 D_MAX=1.13}
 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=1-1728:3
 SIGMA the width to use for the gaussian kernels=0.08
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv3
 REFERENCE_1PDB files with relative distances from central atom=env1c.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2c.pdb
 REFERENCE_3PDB files with relative distances from central atom=env3c.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4c.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=1.00 D_MAX=1.13}
 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
# PLUMED interprets the command:
# ENVIRONMENTSIMILARITY ...
#  SPECIES=1-1728:3
#  SIGMA=0.08
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv3
#  REFERENCE_1=env1c.pdb
#  REFERENCE_2=env2c.pdb
#  REFERENCE_3=env3c.pdb
#  REFERENCE_4=env4c.pdb
#  MORE_THAN={CUBIC D_0=1.00 D_MAX=1.13}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv3_cmatThe DISTANCE_MATRIX action with label refcv3_cmat calculates the following quantities: Quantity    Type    Description  
refcv3_cmat.w matrix a matrix containing the weights for the bonds between each pair of atoms
refcv3_cmat.x matrix the projection of the bond on the x axis
refcv3_cmat.y matrix the projection of the bond on the y axis
refcv3_cmat.z matrix the projection of the bond on the z axis: DISTANCE_MATRIXCalculate a matrix of distances between atoms. More details COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix GROUPthe atoms for which you would like to calculate the adjacency matrix=1-1728:3 CUTOFF ignore distances that have a value larger than this cutoff=0.698694
refcv3_grpThe GROUP action with label refcv3_grp calculates the following quantities: Quantity    Type    Description  
refcv3_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=1-1728:3
refcv3_onesThe CONSTANT action with label refcv3_ones calculates the following quantities: Quantity    Type    Description  
refcv3_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=576
refcv3_matenv1The CUSTOM action with label refcv3_matenv1 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_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(0.698694-w)/16)*(exp(-((x--0.4585)^2+(y--0.0001)^2+(z-0.0019)^2)/(4*0.0064))+exp(-((x--0.2307)^2+(y--0.1316)^2+(z--0.3738)^2)/(4*0.0064))+exp(-((x--0.2296)^2+(y--0.1323)^2+(z--0.093)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3972)^2+(z-0)^2)/(4*0.0064))+exp(-((x--0.2292)^2+(y-0.397)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1314)^2+(z-0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2655)^2+(z--0.3737)^2)/(4*0.0064))+exp(-((x--0.0003)^2+(y-0.2649)^2+(z--0.093)^2)/(4*0.0064))+exp(-((x-0.0012)^2+(y--0.0008)^2+(z-0.2809)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2657)^2+(z-0.3739)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1316)^2+(z--0.3756)^2)/(4*0.0064))+exp(-((x-0.229)^2+(y--0.1323)^2+(z--0.0948)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.397)^2+(z-0)^2)/(4*0.0064))+exp(-((x-0.2294)^2+(y--0.3972)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x-0.2309)^2+(y-0.1314)^2+(z-0.3738)^2)/(4*0.0064))+exp(-((x-0.4586)^2+(y--0.0001)^2+(z--0.0018)^2)/(4*0.0064)))
refcv3_env1The MATRIX_VECTOR_PRODUCT action with label refcv3_env1 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_matenv1,refcv3_ones
refcv3_matenv2The CUSTOM action with label refcv3_matenv2 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_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(0.698694-w)/16)*(exp(-((x--0.4586)^2+(y-0.0001)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x--0.2308)^2+(y--0.1315)^2+(z--0.3739)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3971)^2+(z--0.0001)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y-0.3971)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x--0.229)^2+(y-0.1322)^2+(z-0.0947)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1315)^2+(z-0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2657)^2+(z--0.3739)^2)/(4*0.0064))+exp(-((x--0.0012)^2+(y-0.0008)^2+(z--0.2809)^2)/(4*0.0064))+exp(-((x-0.0003)^2+(y--0.2649)^2+(z-0.093)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2655)^2+(z-0.3737)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1315)^2+(z--0.3757)^2)/(4*0.0064))+exp(-((x-0.2292)^2+(y--0.3971)^2+(z--0.0019)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.3971)^2+(z--0.0001)^2)/(4*0.0064))+exp(-((x-0.2297)^2+(y-0.1322)^2+(z-0.0929)^2)/(4*0.0064))+exp(-((x-0.2307)^2+(y-0.1315)^2+(z-0.3737)^2)/(4*0.0064))+exp(-((x-0.4585)^2+(y-0.0001)^2+(z--0.0019)^2)/(4*0.0064)))
refcv3_env2The MATRIX_VECTOR_PRODUCT action with label refcv3_env2 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_matenv2,refcv3_ones
refcv3_matenv3The CUSTOM action with label refcv3_matenv3 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_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(0.698694-w)/16)*(exp(-((x--0.4585)^2+(y--0.0001)^2+(z--0.0019)^2)/(4*0.0064))+exp(-((x--0.2307)^2+(y--0.1316)^2+(z-0.3738)^2)/(4*0.0064))+exp(-((x--0.2296)^2+(y--0.1323)^2+(z-0.093)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3972)^2+(z--0)^2)/(4*0.0064))+exp(-((x--0.2292)^2+(y-0.397)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1314)^2+(z--0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2655)^2+(z-0.3737)^2)/(4*0.0064))+exp(-((x--0.0003)^2+(y-0.2649)^2+(z-0.093)^2)/(4*0.0064))+exp(-((x-0.0012)^2+(y--0.0008)^2+(z--0.2809)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2657)^2+(z--0.3739)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1316)^2+(z-0.3756)^2)/(4*0.0064))+exp(-((x-0.229)^2+(y--0.1323)^2+(z-0.0948)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.397)^2+(z--0)^2)/(4*0.0064))+exp(-((x-0.2294)^2+(y--0.3972)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x-0.2309)^2+(y-0.1314)^2+(z--0.3738)^2)/(4*0.0064))+exp(-((x-0.4586)^2+(y--0.0001)^2+(z-0.0018)^2)/(4*0.0064)))
refcv3_env3The MATRIX_VECTOR_PRODUCT action with label refcv3_env3 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_matenv3,refcv3_ones
refcv3_matenv4The CUSTOM action with label refcv3_matenv4 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_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(0.698694-w)/16)*(exp(-((x--0.4586)^2+(y-0.0001)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x--0.2308)^2+(y--0.1315)^2+(z-0.3739)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3971)^2+(z-0.0001)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y-0.3971)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x--0.229)^2+(y-0.1322)^2+(z--0.0947)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1315)^2+(z--0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2657)^2+(z-0.3739)^2)/(4*0.0064))+exp(-((x--0.0012)^2+(y-0.0008)^2+(z-0.2809)^2)/(4*0.0064))+exp(-((x-0.0003)^2+(y--0.2649)^2+(z--0.093)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2655)^2+(z--0.3737)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1315)^2+(z-0.3757)^2)/(4*0.0064))+exp(-((x-0.2292)^2+(y--0.3971)^2+(z-0.0019)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.3971)^2+(z-0.0001)^2)/(4*0.0064))+exp(-((x-0.2297)^2+(y-0.1322)^2+(z--0.0929)^2)/(4*0.0064))+exp(-((x-0.2307)^2+(y-0.1315)^2+(z--0.3737)^2)/(4*0.0064))+exp(-((x-0.4585)^2+(y-0.0001)^2+(z-0.0019)^2)/(4*0.0064)))
refcv3_env4The MATRIX_VECTOR_PRODUCT action with label refcv3_env4 calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_matenv4,refcv3_ones
refcv3The CUSTOM action with label refcv3 calculates the following quantities: Quantity    Type    Description  
refcv3 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=refcv3_env1,refcv3_env2,refcv3_env3,refcv3_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))
refcv3_mtThe MORE_THAN action with label refcv3_mt calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={CUBIC D_0=1.00 D_MAX=1.13}
refcv3_morethanThe SUM action with label refcv3_morethan calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
refcv3_meanThe MEAN action with label refcv3_mean calculates the following quantities: Quantity    Type    Description  
refcv3_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=refcv3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
diffThe CUSTOM action with label diff calculates the following quantities: Quantity    Type    Description  
diff scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=refcv.morethan,s.morethan 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

uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities: Quantity    Type    Description  
uwall1.bias scalar the instantaneous value of the bias potential
uwall1.force2 scalar the instantaneous value of the squared force due to this bias potential: 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=50. KAPPAthe force constant for the wall=1.0 EXP the powers for the walls=2 STRIDEthe frequency with which the forces due to the bias should be calculated=2
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: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=refcv3.morethan ATthe positions of the wall=0. KAPPAthe force constant for the wall=20.0 EXP the powers for the walls=2 STRIDEthe frequency with which the forces due to the bias should be calculated=4

diff2The CUSTOM action with label diff2 calculates the following quantities: Quantity    Type    Description  
diff2 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=s.morethan,refcv2.morethan FUNCthe function you wish to evaluate=x/144-y/0.9 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
uwall3The UPPER_WALLS action with label uwall3 calculates the following quantities: Quantity    Type    Description  
uwall3.bias scalar the instantaneous value of the bias potential
uwall3.force2 scalar the instantaneous value of the squared force due to this bias potential: 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. KAPPAthe force constant for the wall=4000.0 EXP the powers for the walls=2 STRIDEthe frequency with which the forces due to the bias should be calculated=2

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=1-1728:3
 SIGMA the width to use for the gaussian kernels=0.065
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv4The ENVIRONMENTSIMILARITY action with label refcv4 calculates the following quantities: Quantity    Type    Description  
refcv4 vector the environmental similar parameter for each of the input atoms
refcv4_morethan scalar the number of colvars that have a value more than a threshold
refcv4_mean scalar the mean of the colvars
 REFERENCE_1PDB files with relative distances from central atom=Large/env1h.pdb
 REFERENCE_2PDB files with relative distances from central atom=Large/env2h.pdb
 REFERENCE_3PDB files with relative distances from central atom=Large/env3h.pdb
 REFERENCE_4PDB files with relative distances from central atom=Large/env4h.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.65 D_MAX=0.67}
 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=1-1728:3
 SIGMA the width to use for the gaussian kernels=0.065
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv4
 REFERENCE_1PDB files with relative distances from central atom=Large/env1h.pdb
 REFERENCE_2PDB files with relative distances from central atom=Large/env2h.pdb
 REFERENCE_3PDB files with relative distances from central atom=Large/env3h.pdb
 REFERENCE_4PDB files with relative distances from central atom=Large/env4h.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.65 D_MAX=0.67}
 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
# PLUMED interprets the command:
# ENVIRONMENTSIMILARITY ...
#  SPECIES=1-1728:3
#  SIGMA=0.065
#  CRYSTAL_STRUCTURE=CUSTOM
#  LABEL=refcv4
#  REFERENCE_1=Large/env1h.pdb
#  REFERENCE_2=Large/env2h.pdb
#  REFERENCE_3=Large/env3h.pdb
#  REFERENCE_4=Large/env4h.pdb
#  MORE_THAN={CUBIC D_0=0.65 D_MAX=0.67}
#  MEAN
# ... ENVIRONMENTSIMILARITY
# as follows (Click the red comment above to revert to the short version of the input):
refcv4_cmatThe DISTANCE_MATRIX action with label refcv4_cmat calculates the following quantities: Quantity    Type    Description  
refcv4_cmat.w matrix a matrix containing the weights for the bonds between each pair of atoms
refcv4_cmat.x matrix the projection of the bond on the x axis
refcv4_cmat.y matrix the projection of the bond on the y axis
refcv4_cmat.z matrix the projection of the bond on the z axis: DISTANCE_MATRIXCalculate a matrix of distances between atoms. More details COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix GROUPthe atoms for which you would like to calculate the adjacency matrix=1-1728:3 CUTOFF ignore distances that have a value larger than this cutoff=0.6535
refcv4_grpThe GROUP action with label refcv4_grp calculates the following quantities: Quantity    Type    Description  
refcv4_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=1-1728:3
refcv4_onesThe CONSTANT action with label refcv4_ones calculates the following quantities: Quantity    Type    Description  
refcv4_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=576
refcv4_matenv1The CUSTOM action with label refcv4_matenv1 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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(0.6535-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225)))
refcv4_env1The MATRIX_VECTOR_PRODUCT action with label refcv4_env1 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_matenv1,refcv4_ones
refcv4_matenv2The CUSTOM action with label refcv4_matenv2 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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(0.6535-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225)))
refcv4_env2The MATRIX_VECTOR_PRODUCT action with label refcv4_env2 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_matenv2,refcv4_ones
refcv4_matenv3The CUSTOM action with label refcv4_matenv3 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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(0.6535-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225)))
refcv4_env3The MATRIX_VECTOR_PRODUCT action with label refcv4_env3 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_matenv3,refcv4_ones
refcv4_matenv4The CUSTOM action with label refcv4_matenv4 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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(0.6535-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225)))
refcv4_env4The MATRIX_VECTOR_PRODUCT action with label refcv4_env4 calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_matenv4,refcv4_ones
refcv4The CUSTOM action with label refcv4 calculates the following quantities: Quantity    Type    Description  
refcv4 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=refcv4_env1,refcv4_env2,refcv4_env3,refcv4_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))
refcv4_mtThe MORE_THAN action with label refcv4_mt calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={CUBIC D_0=0.65 D_MAX=0.67}
refcv4_morethanThe SUM action with label refcv4_morethan calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
refcv4_meanThe MEAN action with label refcv4_mean calculates the following quantities: Quantity    Type    Description  
refcv4_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=refcv4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
s2The AROUND action with label s2 calculates the following quantities: Quantity    Type    Description  
s2_mean scalar the average values of the colvar in the region of interest
s2_morethan scalar the number of cvs in the region of interest that are more than a certain threshold: AROUNDThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. This action is a shortcut. More details DATAthe label of an action that calculates multicolvars=refcv4 ATOMan alternative to ORIGIN=1 ZLOWER the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)=-0.14 ZUPPER the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)=0.14 SIGMAthe width of the function to be used for kernel density estimation=0.001 MEAN calculate the average value of the colvar inside the region of interest MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={CUBIC D_0=0.65 D_MAX=0.67}
# PLUMED interprets the command:
# s2: AROUND DATA=refcv4 ATOM=1 ZLOWER=-0.14 ZUPPER=0.14 SIGMA=0.001 MEAN MORE_THAN={CUBIC D_0=0.65 D_MAX=0.67}
# as follows (Click the red comment above to revert to the short version of the input):
s2_grpThe GROUP action with label s2_grp calculates the following quantities: Quantity    Type    Description  
s2_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=refcv4
s2_prodThe CUSTOM action with label s2_prod calculates the following quantities: Quantity    Type    Description  
s2_prod 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=refcv4,s2 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
s2_numerThe SUM action with label s2_numer calculates the following quantities: Quantity    Type    Description  
s2_numer 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=s2_prod PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
s2_normThe SUM action with label s2_norm calculates the following quantities: Quantity    Type    Description  
s2_norm 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=s2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
s2_meanThe CUSTOM action with label s2_mean calculates the following quantities: Quantity    Type    Description  
s2_mean scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=s2_numer,s2_norm 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
refcv4_s2_mtThe MORE_THAN action with label refcv4_s2_mt calculates the following quantities: Quantity    Type    Description  
refcv4_s2_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=refcv4 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={CUBIC D_0=0.65 D_MAX=0.67}
s2_mtThe CUSTOM action with label s2_mt calculates the following quantities: Quantity    Type    Description  
s2_mt 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=refcv4_s2_mt,s2 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
s2_morethanThe SUM action with label s2_morethan calculates the following quantities: Quantity    Type    Description  
s2_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=s2_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 
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
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
Quantity	Description
.bias	the instantaneous value of the bias potential
.rct	estimate of c(t)
.zed	estimate of Z_n
.neff	effective sample size
.nker	total number of compressed kernels used to represent the bias
PLUMED-NEST

The public repository of the PLUMED consortium
