Shortcut: ENVIRONMENTSIMILARITY
| Module |
envsim |
| Description |
Usage |
| Measure how similar the environment around atoms is to that found in some reference crystal structure. |
  |
| output value |
type |
| the environmental similar parameter for each of the input atoms |
vector |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name |
Type |
Keyword |
Description |
| lessthan |
scalar |
LESS_THAN |
the number of colvars that have a value less than a threshold |
| morethan |
scalar |
MORE_THAN |
the number of colvars that have a value more than a threshold |
| altmin |
scalar |
ALT_MIN |
the minimum value of the cv |
| min |
scalar |
MIN |
the minimum colvar |
| max |
scalar |
MAX |
the maximum colvar |
| between |
scalar |
BETWEEN |
the number of colvars that have a value that lies in a particular interval |
| highest |
scalar |
HIGHEST |
the largest of the colvars |
| lowest |
scalar |
LOWEST |
the smallest of the colvars |
| sum |
scalar |
SUM |
the sum of the colvars |
| mean |
scalar |
MEAN |
the mean of the colvars |
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword |
Type |
Description |
| SPECIES |
atoms |
this keyword is used for colvars such as coordination number |
| SPECIESA |
atoms |
this keyword is used for colvars such as the coordination number |
| SPECIESB |
atoms |
this keyword is used for colvars such as the coordination number |
Further details and examples
Measure how similar the environment around atoms is to that found in some reference crystal structure.
The starting point for the definition of the CV is the local atomic density around an atom.
We consider an environment χ around this atom and we define the density by
ρχ(r)=∑i∈χexp(−|ri−r|22σ2),
where i runs over the neighbors in the environment χ, σ is a broadening parameter, and ri are the
coordinates of the neighbors relative to the central atom.
We now define a reference environment or template χ0 that contains n reference positions {r01,...,r0n}
that describe, for instance, the nearest neighbors in a given lattice.
σ is set using the SIGMA keyword and χ0 is chosen with the CRYSTAL_STRUCTURE keyword.
If only the SPECIES keyword is given then the atoms defined there will be the central and neighboring atoms.
If instead the SPECIESA and SPECIESB keywords are given then SPECIESA determines the central atoms and SPECIESB the neighbors.
The environments χ and χ0 are compared using the kernel,
kχ0(χ)=∫drρχ(r)ρχ0(r).
Combining the two equations above and performing the integration analytically we obtain,
kχ0(χ)=∑i∈χ∑j∈χ0π3/2σ3exp(−|ri−r0j|24σ2).
The kernel is finally normalized,
˜kχ0(χ)=1n∑i∈χ∑j∈χ0exp(−|ri−r0j|24σ2),
such that ˜kχ0(χ0)=1.
The above kernel is computed for each atom in the SPECIES or SPECIESA keywords.
This quantity is a multicolvar so you can compute it for multiple atoms using a single PLUMED action and then compute
the average value for the atoms in your system, the number of atoms that have an ˜kχ0 value that is more that some target and
so on.
The kernel can be generalized to crystal structures described as a lattice with a basis of more than one atom.
In this case there is more than one type of environment.
We consider the case of M environments X=χ1,χ2,...,χM and we define the kernel through a best match strategy:
˜kX(χ)=1λlog(M∑l=1exp(λ˜kχl(χ))).
For a large enough λ this expression will select the largest ˜kχl(χ) with χl∈X.
This approach can be used, for instance, to target the hexagonal closed packed (HCP keyword) or the diamond structure (DIAMOND keyword).
The CRYSTAL_STRUCTURE keyword can take the values SC (simple cubic), BCC (body centered cubic), FCC (face centered cubic),
HCP (hexagonal closed pack), DIAMOND (cubic diamond), and CUSTOM (user defined).
All options follow the same conventions as in the lattice command of LAMMPS.
If a CRYSTAL_STRUCTURE other than CUSTOM is used, then the lattice constants have to be specified using the keyword LATTICE_CONSTANTS.
One value has to be specified for SC, BCC, FCC, and DIAMOND and two values have to be set for HCP (a and c lattice constants in that order).
If the CUSTOM option is used then the reference environments have to be specified by the user.
The reference environments are specified in pdb files containing the distance vectors from the central atom to the neighbors.
Make sure your PDB file is correctly formatted as explained in the documenation for MOLINFO
If only one reference environment is specified then the filename should be given as argument of the keyword REFERENCE.
If instead several reference environments are given, then they have to be provided in separate pdb files and given as arguments for the
keywords REFERENCE_1, REFERENCE_2, etc.
If you have a reference crystal structure configuration you can use the Environment Finder app to determine the reference environments that you should use.
If multiple chemical species are involved in the calculation, it is possible to provide the atom types (names) both for atoms in the reference environments and in the simulation box.
This information is provided in pdb files using the atom name field.
The comparison between environments is performed taking into account whether the atom names match.
Examples
The following input calculates the ENVIRONMENTSIMILARITY kernel for 250 atoms in the system
using the BCC atomic environment as target, and then calculates and prints the average value
for this quantity.
Click on the labels of the actions for more information on what each action computes
esThe ENVIRONMENTSIMILARITY action with label es calculates the following quantities:| Quantity | Type | Description |
| es | vector | the environmental similar parameter for each of the input atoms |
| es_mean | scalar | the mean of the colvars |
: 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=1-250 SIGMA the width to use for the gaussian kernels=0.05 LATTICE_CONSTANTSLattice constants=0.423 CRYSTAL_STRUCTURE Targeted crystal structure=BCC MEAN calculate the mean of all the quantities
es: 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=1-250 SIGMA the width to use for the gaussian kernels=0.05 LATTICE_CONSTANTSLattice constants=0.423 CRYSTAL_STRUCTURE Targeted crystal structure=BCC 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
# es: ENVIRONMENTSIMILARITY SPECIES=1-250 SIGMA=0.05 LATTICE_CONSTANTS=0.423 CRYSTAL_STRUCTURE=BCC MEAN
es_cmatThe DISTANCE_MATRIX action with label es_cmat calculates the following quantities:| Quantity | Type | Description |
| es_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| es_cmat.x | matrix | the projection of the bond on the x axis |
| es_cmat.y | matrix | the projection of the bond on the y axis |
| es_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=1-250 CUTOFF ignore distances that have a value larger than this cutoff=0.573
es_grpThe GROUP action with label es_grp calculates the following quantities:| Quantity | Type | Description |
| es_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=1-250
es_onesThe CONSTANT action with label es_ones calculates the following quantities:| Quantity | Type | Description |
| es_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=250
es_matenv1The CUSTOM action with label es_matenv1 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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(0.573-w)/14)*(exp(-((x-0.2115)^2+(y-0.2115)^2+(z-0.2115)^2)/(4*0.0025))+exp(-((x--0.2115)^2+(y--0.2115)^2+(z--0.2115)^2)/(4*0.0025))+exp(-((x--0.2115)^2+(y-0.2115)^2+(z-0.2115)^2)/(4*0.0025))+exp(-((x-0.2115)^2+(y--0.2115)^2+(z-0.2115)^2)/(4*0.0025))+exp(-((x-0.2115)^2+(y-0.2115)^2+(z--0.2115)^2)/(4*0.0025))+exp(-((x--0.2115)^2+(y--0.2115)^2+(z-0.2115)^2)/(4*0.0025))+exp(-((x-0.2115)^2+(y--0.2115)^2+(z--0.2115)^2)/(4*0.0025))+exp(-((x--0.2115)^2+(y-0.2115)^2+(z--0.2115)^2)/(4*0.0025))+exp(-((x-0.423)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.423)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z-0.423)^2)/(4*0.0025))+exp(-((x--0.423)^2+(y-0)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.423)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0)^2+(z--0.423)^2)/(4*0.0025)))
esThe MATRIX_VECTOR_PRODUCT action with label es calculates the following quantities:| Quantity | Type | Description |
| es | 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=es_matenv1,es_ones
es_meanThe MEAN action with label es_mean calculates the following quantities:| Quantity | Type | Description |
| es_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=es 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 ARGthe labels of the values that you would like to print to the file=es.mean FILEthe name of the file on which to output these quantities=COLVAR
The next example compares the environments of the 96 selected atoms with a user specified reference
environment. The reference environment is contained in the env1.pdb file. Once the kernel is computed
the average and the number of atoms with a kernel larger than 0.5 are computed.
Click on the labels of the actions for more information on what each action computes
esThe ENVIRONMENTSIMILARITY action with label es calculates the following quantities:| Quantity | Type | Description |
| es | vector | the environmental similar parameter for each of the input atoms |
| es_morethan | scalar | the number of colvars that have a value more than a threshold |
| es_mean | scalar | the mean of the colvars |
: 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=1-288:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
REFERENCEPDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 -1.296 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 -0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.296 -0.917 1.00 0.00 O
MEAN calculate the mean of all the quantities
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.={RATIONAL R_0=0.5 NN=12 MM=24}
...
es: 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=1-288:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
REFERENCEPDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 -1.296 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 -0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.296 -0.917 1.00 0.00 O
MEAN calculate the mean of all the quantities
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.={RATIONAL R_0=0.5 NN=12 MM=24}
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
...
# es: ENVIRONMENTSIMILARITY ...
es_cmatThe DISTANCE_MATRIX action with label es_cmat calculates the following quantities:| Quantity | Type | Description |
| es_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| es_cmat.x | matrix | the projection of the bond on the x axis |
| es_cmat.y | matrix | the projection of the bond on the y axis |
| es_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=1-288:3 CUTOFF ignore distances that have a value larger than this cutoff=0.425131
es_grpThe GROUP action with label es_grp calculates the following quantities:| Quantity | Type | Description |
| es_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=1-288:3
es_onesThe CONSTANT action with label es_ones calculates the following quantities:| Quantity | Type | Description |
| es_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=96
es_matenv1The CUSTOM action with label es_matenv1 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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(0.425131-w)/4)*(exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^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--0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.0025)))
esThe MATRIX_VECTOR_PRODUCT action with label es calculates the following quantities:| Quantity | Type | Description |
| es | 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=es_matenv1,es_ones
es_mtThe MORE_THAN action with label es_mt calculates the following quantities:| Quantity | Type | Description |
| es_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=es SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.5 NN=12 MM=24}
es_morethanThe SUM action with label es_morethan calculates the following quantities:| Quantity | Type | Description |
| es_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=es_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
es_meanThe MEAN action with label es_mean calculates the following quantities:| Quantity | Type | Description |
| es_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=es 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 ARGthe labels of the values that you would like to print to the file=es.mean,es.morethan FILEthe name of the file on which to output these quantities=COLVAR
The next example is similar to the one above but in this case 4 reference environments are specified.
Each reference environment is given in a separate pdb file.
Click on the labels of the actions for more information on what each action computes
esThe ENVIRONMENTSIMILARITY action with label es calculates the following quantities:| Quantity | Type | Description |
| es | vector | the environmental similar parameter for each of the input atoms |
| es_morethan | scalar | the number of colvars that have a value more than a threshold |
| es_mean | scalar | the mean of the colvars |
: 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=1-288:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
REFERENCE_1PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 -1.296 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 -0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.296 -0.917 1.00 0.00 O
REFERENCE_2PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 1.297 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 -2.594 -0.917 1.00 0.00 O
ATOM 3 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 4 O MOL 1 2.246 1.297 -0.917 1.00 0.00 O
REFERENCE_3PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.246 1.296 0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 -2.594 0.917 1.00 0.00 O
ATOM 3 O MOL 1 0.000 0.000 -2.751 1.00 0.00 O
ATOM 4 O MOL 1 2.246 1.296 0.917 1.00 0.00 O
REFERENCE_4PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.246 -1.297 0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 -2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.297 0.917 1.00 0.00 O
MEAN calculate the mean of all the quantities
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.={RATIONAL R_0=0.5 NN=12 MM=24}
...
es: 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=1-288:3
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
REFERENCE_1PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 -1.296 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 -0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.296 -0.917 1.00 0.00 O
REFERENCE_2PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 1.297 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 -2.594 -0.917 1.00 0.00 O
ATOM 3 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 4 O MOL 1 2.246 1.297 -0.917 1.00 0.00 O
REFERENCE_3PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.246 1.296 0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 -2.594 0.917 1.00 0.00 O
ATOM 3 O MOL 1 0.000 0.000 -2.751 1.00 0.00 O
ATOM 4 O MOL 1 2.246 1.296 0.917 1.00 0.00 O
REFERENCE_4PDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.246 -1.297 0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 -2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.297 0.917 1.00 0.00 O
MEAN calculate the mean of all the quantities
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.={RATIONAL R_0=0.5 NN=12 MM=24}
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
...
# es: ENVIRONMENTSIMILARITY ...
es_cmatThe DISTANCE_MATRIX action with label es_cmat calculates the following quantities:| Quantity | Type | Description |
| es_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| es_cmat.x | matrix | the projection of the bond on the x axis |
| es_cmat.y | matrix | the projection of the bond on the y axis |
| es_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=1-288:3 CUTOFF ignore distances that have a value larger than this cutoff=0.425131
es_grpThe GROUP action with label es_grp calculates the following quantities:| Quantity | Type | Description |
| es_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=1-288:3
es_onesThe CONSTANT action with label es_ones calculates the following quantities:| Quantity | Type | Description |
| es_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=96
es_matenv1The CUSTOM action with label es_matenv1 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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(0.425131-w)/4)*(exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^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--0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.0025)))
es_env1The MATRIX_VECTOR_PRODUCT action with label es_env1 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_matenv1,es_ones
es_matenv2The CUSTOM action with label es_matenv2 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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(0.425131-w)/4)*(exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^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)^2+(z-0.2751)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.0025)))
es_env2The MATRIX_VECTOR_PRODUCT action with label es_env2 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_matenv2,es_ones
es_matenv3The CUSTOM action with label es_matenv3 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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(0.425131-w)/4)*(exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^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)^2+(z--0.2751)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.0025)))
es_env3The MATRIX_VECTOR_PRODUCT action with label es_env3 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_matenv3,es_ones
es_matenv4The CUSTOM action with label es_matenv4 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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(0.425131-w)/4)*(exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^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-0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.0025)))
es_env4The MATRIX_VECTOR_PRODUCT action with label es_env4 calculates the following quantities:| Quantity | Type | Description |
| es_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=es_matenv4,es_ones
esThe CUSTOM action with label es calculates the following quantities:| Quantity | Type | Description |
| es | 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=es_env1,es_env2,es_env3,es_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))
es_mtThe MORE_THAN action with label es_mt calculates the following quantities:| Quantity | Type | Description |
| es_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=es SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.5 NN=12 MM=24}
es_morethanThe SUM action with label es_morethan calculates the following quantities:| Quantity | Type | Description |
| es_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=es_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
es_meanThe MEAN action with label es_mean calculates the following quantities:| Quantity | Type | Description |
| es_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=es 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 ARGthe labels of the values that you would like to print to the file=es.mean,es.morethan FILEthe name of the file on which to output these quantities=COLVAR
The following examples illustrates the use of pdb files to provide information about different chemical species:
Click on the labels of the actions for more information on what each action computes
esThe ENVIRONMENTSIMILARITY action with label es calculates the following quantities:| Quantity | Type | Description |
| es | vector | the environmental similar parameter for each of the input atoms |
| es_morethan | scalar | the number of colvars that have a value more than a threshold |
| es_mean | scalar | the mean of the colvars |
: 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=1-384
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
REFERENCEPDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 -1.296 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 -0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.296 -0.917 1.00 0.00 O
MEAN calculate the mean of all the quantities
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.={RATIONAL R_0=0.5 NN=12 MM=24}
ATOM_NAMES_FILEPDB file with atom names for all atoms in SPECIES= CRYST1 13.470 15.562 14.672 90.00 90.00 90.00 P 1 1
ATOM 1 O X 1 0.000 2.593 4.126 0.00 0.00 O
ATOM 4 O X 1 0.000 2.593 11.462 0.00 0.00 O
ATOM 7 O X 1 0.000 10.374 4.126 0.00 0.00 O
ATOM 10 O X 1 0.000 10.374 11.462 0.00 0.00 O
ATOM 13 O X 1 4.492 2.593 4.126 0.00 0.00 O
ATOM 16 O X 1 4.492 2.593 11.462 0.00 0.00 O
ATOM 19 O X 1 4.492 10.374 4.126 0.00 0.00 O
ATOM 22 O X 1 4.492 10.374 11.462 0.00 0.00 O
ATOM 25 O X 1 8.984 2.593 4.126 0.00 0.00 O
ATOM 28 O X 1 8.984 2.593 11.462 0.00 0.00 O
ATOM 31 O X 1 8.984 10.374 4.126 0.00 0.00 O
ATOM 34 O X 1 8.984 10.374 11.462 0.00 0.00 O
ATOM 37 O X 1 2.246 6.484 4.126 0.00 0.00 O
ATOM 40 O X 1 2.246 6.484 11.462 0.00 0.00 O
ATOM 43 O X 1 2.246 14.265 4.126 0.00 0.00 O
ATOM 46 O X 1 2.246 14.265 11.462 0.00 0.00 O
ATOM 49 O X 1 6.738 6.484 4.126 0.00 0.00 O
ATOM 52 O X 1 6.738 6.484 11.462 0.00 0.00 O
ATOM 55 O X 1 6.738 14.265 4.126 0.00 0.00 O
ATOM 58 O X 1 6.738 14.265 11.462 0.00 0.00 O
ATOM 61 O X 1 11.231 6.484 4.126 0.00 0.00 O
ATOM 64 O X 1 11.231 6.484 11.462 0.00 0.00 O
ATOM 67 O X 1 11.231 14.265 4.126 0.00 0.00 O
ATOM 70 O X 1 11.231 14.265 11.462 0.00 0.00 O
ATOM 73 O X 1 0.000 5.187 7.794 0.00 0.00 O
ATOM 76 O X 1 0.000 5.187 15.130 0.00 0.00 O
ATOM 79 O X 1 0.000 12.968 7.794 0.00 0.00 O
ATOM 82 O X 1 0.000 12.968 15.130 0.00 0.00 O
ATOM 85 O X 1 4.492 5.187 7.794 0.00 0.00 O
ATOM 88 O X 1 4.492 5.187 15.130 0.00 0.00 O
ATOM 91 O X 1 4.492 12.968 7.794 0.00 0.00 O
ATOM 94 O X 1 4.492 12.968 15.130 0.00 0.00 O
ATOM 97 O X 1 8.984 5.187 7.794 0.00 0.00 O
ATOM 100 O X 1 8.984 5.187 15.130 0.00 0.00 O
ATOM 103 O X 1 8.984 12.968 7.794 0.00 0.00 O
ATOM 106 O X 1 8.984 12.968 15.130 0.00 0.00 O
ATOM 109 O X 1 2.246 1.297 7.794 0.00 0.00 O
ATOM 112 O X 1 2.246 1.297 15.130 0.00 0.00 O
ATOM 115 O X 1 2.246 9.078 7.794 0.00 0.00 O
ATOM 118 O X 1 2.246 9.078 15.130 0.00 0.00 O
ATOM 121 O X 1 6.738 1.297 7.794 0.00 0.00 O
ATOM 124 O X 1 6.738 1.297 15.130 0.00 0.00 O
ATOM 127 O X 1 6.738 9.078 7.794 0.00 0.00 O
ATOM 130 O X 1 6.738 9.078 15.130 0.00 0.00 O
ATOM 133 O X 1 11.231 1.297 7.794 0.00 0.00 O
ATOM 136 O X 1 11.231 1.297 15.130 0.00 0.00 O
ATOM 139 O X 1 11.231 9.078 7.794 0.00 0.00 O
ATOM 142 O X 1 11.231 9.078 15.130 0.00 0.00 O
ATOM 145 O X 1 2.246 1.297 3.209 0.00 0.00 O
ATOM 148 O X 1 2.246 1.297 10.545 0.00 0.00 O
ATOM 151 O X 1 2.246 9.078 3.209 0.00 0.00 O
ATOM 154 O X 1 2.246 9.078 10.545 0.00 0.00 O
ATOM 157 O X 1 6.738 1.297 3.209 0.00 0.00 O
ATOM 160 O X 1 6.738 1.297 10.545 0.00 0.00 O
ATOM 163 O X 1 6.738 9.078 3.209 0.00 0.00 O
ATOM 166 O X 1 6.738 9.078 10.545 0.00 0.00 O
ATOM 169 O X 1 11.231 1.297 3.209 0.00 0.00 O
ATOM 172 O X 1 11.231 1.297 10.545 0.00 0.00 O
ATOM 175 O X 1 11.231 9.078 3.209 0.00 0.00 O
ATOM 178 O X 1 11.231 9.078 10.545 0.00 0.00 O
ATOM 181 O X 1 0.000 5.187 3.209 0.00 0.00 O
ATOM 184 O X 1 0.000 5.187 10.545 0.00 0.00 O
ATOM 187 O X 1 0.000 12.968 3.209 0.00 0.00 O
ATOM 190 O X 1 0.000 12.968 10.545 0.00 0.00 O
ATOM 193 O X 1 4.492 5.187 3.209 0.00 0.00 O
ATOM 196 O X 1 4.492 5.187 10.545 0.00 0.00 O
ATOM 199 O X 1 4.492 12.968 3.209 0.00 0.00 O
ATOM 202 O X 1 4.492 12.968 10.545 0.00 0.00 O
ATOM 205 O X 1 8.984 5.187 3.209 0.00 0.00 O
ATOM 208 O X 1 8.984 5.187 10.545 0.00 0.00 O
ATOM 211 O X 1 8.984 12.968 3.209 0.00 0.00 O
ATOM 214 O X 1 8.984 12.968 10.545 0.00 0.00 O
ATOM 217 O X 1 2.246 6.484 6.877 0.00 0.00 O
ATOM 220 O X 1 2.246 6.484 14.213 0.00 0.00 O
ATOM 223 O X 1 2.246 14.265 6.877 0.00 0.00 O
ATOM 226 O X 1 2.246 14.265 14.213 0.00 0.00 O
ATOM 229 O X 1 6.738 6.484 6.877 0.00 0.00 O
ATOM 232 O X 1 6.738 6.484 14.213 0.00 0.00 O
ATOM 235 O X 1 6.738 14.265 6.877 0.00 0.00 O
ATOM 238 O X 1 6.738 14.265 14.213 0.00 0.00 O
ATOM 241 O X 1 11.231 6.484 6.877 0.00 0.00 O
ATOM 244 O X 1 11.231 6.484 14.213 0.00 0.00 O
ATOM 247 O X 1 11.231 14.265 6.877 0.00 0.00 O
ATOM 250 O X 1 11.231 14.265 14.213 0.00 0.00 O
ATOM 253 O X 1 0.000 2.593 6.877 0.00 0.00 O
ATOM 256 O X 1 0.000 2.593 14.213 0.00 0.00 O
ATOM 259 O X 1 0.000 10.374 6.877 0.00 0.00 O
ATOM 262 O X 1 0.000 10.374 14.213 0.00 0.00 O
ATOM 265 O X 1 4.492 2.593 6.877 0.00 0.00 O
ATOM 268 O X 1 4.492 2.593 14.213 0.00 0.00 O
ATOM 271 O X 1 4.492 10.374 6.877 0.00 0.00 O
ATOM 274 O X 1 4.492 10.374 14.213 0.00 0.00 O
ATOM 277 O X 1 8.984 2.593 6.877 0.00 0.00 O
ATOM 280 O X 1 8.984 2.593 14.213 0.00 0.00 O
ATOM 283 O X 1 8.984 10.374 6.877 0.00 0.00 O
ATOM 286 O X 1 8.984 10.374 14.213 0.00 0.00 O
ATOM 1 O X 1 0.000 2.593 4.126 0.00 0.00 O
ATOM 2 H X 1 0.000 3.509 3.847 0.00 0.00 H
ATOM 3 H X 1 0.000 2.635 5.083 0.00 0.00 H
ATOM 4 O X 1 0.000 2.593 11.462 0.00 0.00 O
ATOM 5 H X 1 0.000 3.509 11.183 0.00 0.00 H
ATOM 6 H X 1 0.000 2.635 12.419 0.00 0.00 H
ATOM 7 O X 1 0.000 10.374 4.126 0.00 0.00 O
ATOM 8 H X 1 0.000 11.290 3.847 0.00 0.00 H
ATOM 9 H X 1 0.000 10.415 5.083 0.00 0.00 H
ATOM 10 O X 1 0.000 10.374 11.462 0.00 0.00 O
ATOM 11 H X 1 0.000 11.290 11.183 0.00 0.00 H
ATOM 12 H X 1 0.000 10.415 12.419 0.00 0.00 H
ATOM 13 O X 1 4.492 2.593 4.126 0.00 0.00 O
ATOM 14 H X 1 4.492 3.509 3.847 0.00 0.00 H
ATOM 15 H X 1 4.492 2.635 5.083 0.00 0.00 H
ATOM 16 O X 1 4.492 2.593 11.462 0.00 0.00 O
ATOM 17 H X 1 4.492 3.509 11.183 0.00 0.00 H
ATOM 18 H X 1 4.492 2.635 12.419 0.00 0.00 H
ATOM 19 O X 1 4.492 10.374 4.126 0.00 0.00 O
ATOM 20 H X 1 4.492 11.290 3.847 0.00 0.00 H
ATOM 21 H X 1 4.492 10.415 5.083 0.00 0.00 H
ATOM 22 O X 1 4.492 10.374 11.462 0.00 0.00 O
ATOM 23 H X 1 4.492 11.290 11.183 0.00 0.00 H
ATOM 24 H X 1 4.492 10.415 12.419 0.00 0.00 H
ATOM 25 O X 1 8.984 2.593 4.126 0.00 0.00 O
ATOM 26 H X 1 8.984 3.509 3.847 0.00 0.00 H
ATOM 27 H X 1 8.984 2.635 5.083 0.00 0.00 H
ATOM 28 O X 1 8.984 2.593 11.462 0.00 0.00 O
ATOM 29 H X 1 8.984 3.509 11.183 0.00 0.00 H
ATOM 30 H X 1 8.984 2.635 12.419 0.00 0.00 H
ATOM 31 O X 1 8.984 10.374 4.126 0.00 0.00 O
ATOM 32 H X 1 8.984 11.290 3.847 0.00 0.00 H
ATOM 33 H X 1 8.984 10.415 5.083 0.00 0.00 H
ATOM 34 O X 1 8.984 10.374 11.462 0.00 0.00 O
ATOM 35 H X 1 8.984 11.290 11.183 0.00 0.00 H
ATOM 36 H X 1 8.984 10.415 12.419 0.00 0.00 H
ATOM 37 O X 1 2.246 6.484 4.126 0.00 0.00 O
ATOM 38 H X 1 2.246 7.400 3.847 0.00 0.00 H
ATOM 39 H X 1 2.246 6.525 5.083 0.00 0.00 H
ATOM 40 O X 1 2.246 6.484 11.462 0.00 0.00 O
ATOM 41 H X 1 2.246 7.400 11.183 0.00 0.00 H
ATOM 42 H X 1 2.246 6.525 12.419 0.00 0.00 H
ATOM 43 O X 1 2.246 14.265 4.126 0.00 0.00 O
ATOM 44 H X 1 2.246 15.180 3.847 0.00 0.00 H
ATOM 45 H X 1 2.246 14.306 5.083 0.00 0.00 H
ATOM 46 O X 1 2.246 14.265 11.462 0.00 0.00 O
ATOM 47 H X 1 2.246 15.180 11.183 0.00 0.00 H
ATOM 48 H X 1 2.246 14.306 12.419 0.00 0.00 H
ATOM 49 O X 1 6.738 6.484 4.126 0.00 0.00 O
ATOM 50 H X 1 6.738 7.400 3.847 0.00 0.00 H
ATOM 51 H X 1 6.738 6.525 5.083 0.00 0.00 H
ATOM 52 O X 1 6.738 6.484 11.462 0.00 0.00 O
ATOM 53 H X 1 6.738 7.400 11.183 0.00 0.00 H
ATOM 54 H X 1 6.738 6.525 12.419 0.00 0.00 H
ATOM 55 O X 1 6.738 14.265 4.126 0.00 0.00 O
ATOM 56 H X 1 6.738 15.180 3.847 0.00 0.00 H
ATOM 57 H X 1 6.738 14.306 5.083 0.00 0.00 H
ATOM 58 O X 1 6.738 14.265 11.462 0.00 0.00 O
ATOM 59 H X 1 6.738 15.180 11.183 0.00 0.00 H
ATOM 60 H X 1 6.738 14.306 12.419 0.00 0.00 H
ATOM 61 O X 1 11.231 6.484 4.126 0.00 0.00 O
ATOM 62 H X 1 11.231 7.400 3.847 0.00 0.00 H
ATOM 63 H X 1 11.231 6.525 5.083 0.00 0.00 H
ATOM 64 O X 1 11.231 6.484 11.462 0.00 0.00 O
ATOM 65 H X 1 11.231 7.400 11.183 0.00 0.00 H
ATOM 66 H X 1 11.231 6.525 12.419 0.00 0.00 H
ATOM 67 O X 1 11.231 14.265 4.126 0.00 0.00 O
ATOM 68 H X 1 11.231 15.180 3.847 0.00 0.00 H
ATOM 69 H X 1 11.231 14.306 5.083 0.00 0.00 H
ATOM 70 O X 1 11.231 14.265 11.462 0.00 0.00 O
ATOM 71 H X 1 11.231 15.180 11.183 0.00 0.00 H
ATOM 72 H X 1 11.231 14.306 12.419 0.00 0.00 H
ATOM 73 O X 1 0.000 5.187 7.794 0.00 0.00 O
ATOM 74 H X 1 0.000 4.272 7.515 0.00 0.00 H
ATOM 75 H X 1 0.000 5.146 8.751 0.00 0.00 H
ATOM 76 O X 1 0.000 5.187 15.130 0.00 0.00 O
ATOM 77 H X 1 0.000 4.272 14.851 0.00 0.00 H
ATOM 78 H X 1 0.000 5.146 16.087 0.00 0.00 H
ATOM 79 O X 1 0.000 12.968 7.794 0.00 0.00 O
ATOM 80 H X 1 0.000 12.052 7.515 0.00 0.00 H
ATOM 81 H X 1 0.000 12.927 8.751 0.00 0.00 H
ATOM 82 O X 1 0.000 12.968 15.130 0.00 0.00 O
ATOM 83 H X 1 0.000 12.052 14.851 0.00 0.00 H
ATOM 84 H X 1 0.000 12.927 16.087 0.00 0.00 H
ATOM 85 O X 1 4.492 5.187 7.794 0.00 0.00 O
ATOM 86 H X 1 4.492 4.272 7.515 0.00 0.00 H
ATOM 87 H X 1 4.492 5.146 8.751 0.00 0.00 H
ATOM 88 O X 1 4.492 5.187 15.130 0.00 0.00 O
ATOM 89 H X 1 4.492 4.272 14.851 0.00 0.00 H
ATOM 90 H X 1 4.492 5.146 16.087 0.00 0.00 H
ATOM 91 O X 1 4.492 12.968 7.794 0.00 0.00 O
ATOM 92 H X 1 4.492 12.052 7.515 0.00 0.00 H
ATOM 93 H X 1 4.492 12.927 8.751 0.00 0.00 H
ATOM 94 O X 1 4.492 12.968 15.130 0.00 0.00 O
ATOM 95 H X 1 4.492 12.052 14.851 0.00 0.00 H
ATOM 96 H X 1 4.492 12.927 16.087 0.00 0.00 H
ATOM 97 O X 1 8.984 5.187 7.794 0.00 0.00 O
ATOM 98 H X 1 8.984 4.272 7.515 0.00 0.00 H
ATOM 99 H X 1 8.984 5.146 8.751 0.00 0.00 H
ATOM 100 O X 1 8.984 5.187 15.130 0.00 0.00 O
ATOM 101 H X 1 8.984 4.272 14.851 0.00 0.00 H
ATOM 102 H X 1 8.984 5.146 16.087 0.00 0.00 H
ATOM 103 O X 1 8.984 12.968 7.794 0.00 0.00 O
ATOM 104 H X 1 8.984 12.052 7.515 0.00 0.00 H
ATOM 105 H X 1 8.984 12.927 8.751 0.00 0.00 H
ATOM 106 O X 1 8.984 12.968 15.130 0.00 0.00 O
ATOM 107 H X 1 8.984 12.052 14.851 0.00 0.00 H
ATOM 108 H X 1 8.984 12.927 16.087 0.00 0.00 H
ATOM 109 O X 1 2.246 1.297 7.794 0.00 0.00 O
ATOM 110 H X 1 2.246 0.381 7.515 0.00 0.00 H
ATOM 111 H X 1 2.246 1.256 8.751 0.00 0.00 H
ATOM 112 O X 1 2.246 1.297 15.130 0.00 0.00 O
ATOM 113 H X 1 2.246 0.381 14.851 0.00 0.00 H
ATOM 114 H X 1 2.246 1.256 16.087 0.00 0.00 H
ATOM 115 O X 1 2.246 9.078 7.794 0.00 0.00 O
ATOM 116 H X 1 2.246 8.162 7.515 0.00 0.00 H
ATOM 117 H X 1 2.246 9.037 8.751 0.00 0.00 H
ATOM 118 O X 1 2.246 9.078 15.130 0.00 0.00 O
ATOM 119 H X 1 2.246 8.162 14.851 0.00 0.00 H
ATOM 120 H X 1 2.246 9.037 16.087 0.00 0.00 H
ATOM 121 O X 1 6.738 1.297 7.794 0.00 0.00 O
ATOM 122 H X 1 6.738 0.381 7.515 0.00 0.00 H
ATOM 123 H X 1 6.738 1.256 8.751 0.00 0.00 H
ATOM 124 O X 1 6.738 1.297 15.130 0.00 0.00 O
ATOM 125 H X 1 6.738 0.381 14.851 0.00 0.00 H
ATOM 126 H X 1 6.738 1.256 16.087 0.00 0.00 H
ATOM 127 O X 1 6.738 9.078 7.794 0.00 0.00 O
ATOM 128 H X 1 6.738 8.162 7.515 0.00 0.00 H
ATOM 129 H X 1 6.738 9.037 8.751 0.00 0.00 H
ATOM 130 O X 1 6.738 9.078 15.130 0.00 0.00 O
ATOM 131 H X 1 6.738 8.162 14.851 0.00 0.00 H
ATOM 132 H X 1 6.738 9.037 16.087 0.00 0.00 H
ATOM 133 O X 1 11.231 1.297 7.794 0.00 0.00 O
ATOM 134 H X 1 11.231 0.381 7.515 0.00 0.00 H
ATOM 135 H X 1 11.231 1.256 8.751 0.00 0.00 H
ATOM 136 O X 1 11.231 1.297 15.130 0.00 0.00 O
ATOM 137 H X 1 11.231 0.381 14.851 0.00 0.00 H
ATOM 138 H X 1 11.231 1.256 16.087 0.00 0.00 H
ATOM 139 O X 1 11.231 9.078 7.794 0.00 0.00 O
ATOM 140 H X 1 11.231 8.162 7.515 0.00 0.00 H
ATOM 141 H X 1 11.231 9.037 8.751 0.00 0.00 H
ATOM 142 O X 1 11.231 9.078 15.130 0.00 0.00 O
ATOM 143 H X 1 11.231 8.162 14.851 0.00 0.00 H
ATOM 144 H X 1 11.231 9.037 16.087 0.00 0.00 H
ATOM 145 O X 1 2.246 1.297 3.209 0.00 0.00 O
ATOM 146 H X 1 3.003 1.776 3.548 0.00 0.00 H
ATOM 147 H X 1 1.489 1.776 3.548 0.00 0.00 H
ATOM 148 O X 1 2.246 1.297 10.545 0.00 0.00 O
ATOM 149 H X 1 3.003 1.776 10.883 0.00 0.00 H
ATOM 150 H X 1 1.489 1.776 10.883 0.00 0.00 H
ATOM 151 O X 1 2.246 9.078 3.209 0.00 0.00 O
ATOM 152 H X 1 3.003 9.556 3.548 0.00 0.00 H
ATOM 153 H X 1 1.489 9.556 3.548 0.00 0.00 H
ATOM 154 O X 1 2.246 9.078 10.545 0.00 0.00 O
ATOM 155 H X 1 3.003 9.556 10.883 0.00 0.00 H
ATOM 156 H X 1 1.489 9.556 10.883 0.00 0.00 H
ATOM 157 O X 1 6.738 1.297 3.209 0.00 0.00 O
ATOM 158 H X 1 7.495 1.776 3.548 0.00 0.00 H
ATOM 159 H X 1 5.981 1.776 3.548 0.00 0.00 H
ATOM 160 O X 1 6.738 1.297 10.545 0.00 0.00 O
ATOM 161 H X 1 7.495 1.776 10.883 0.00 0.00 H
ATOM 162 H X 1 5.981 1.776 10.883 0.00 0.00 H
ATOM 163 O X 1 6.738 9.078 3.209 0.00 0.00 O
ATOM 164 H X 1 7.495 9.556 3.548 0.00 0.00 H
ATOM 165 H X 1 5.981 9.556 3.548 0.00 0.00 H
ATOM 166 O X 1 6.738 9.078 10.545 0.00 0.00 O
ATOM 167 H X 1 7.495 9.556 10.883 0.00 0.00 H
ATOM 168 H X 1 5.981 9.556 10.883 0.00 0.00 H
ATOM 169 O X 1 11.231 1.297 3.209 0.00 0.00 O
ATOM 170 H X 1 11.988 1.776 3.548 0.00 0.00 H
ATOM 171 H X 1 10.474 1.776 3.548 0.00 0.00 H
ATOM 172 O X 1 11.231 1.297 10.545 0.00 0.00 O
ATOM 173 H X 1 11.988 1.776 10.883 0.00 0.00 H
ATOM 174 H X 1 10.474 1.776 10.883 0.00 0.00 H
ATOM 175 O X 1 11.231 9.078 3.209 0.00 0.00 O
ATOM 176 H X 1 11.988 9.556 3.548 0.00 0.00 H
ATOM 177 H X 1 10.474 9.556 3.548 0.00 0.00 H
ATOM 178 O X 1 11.231 9.078 10.545 0.00 0.00 O
ATOM 179 H X 1 11.988 9.556 10.883 0.00 0.00 H
ATOM 180 H X 1 10.474 9.556 10.883 0.00 0.00 H
ATOM 181 O X 1 0.000 5.187 3.209 0.00 0.00 O
ATOM 182 H X 1 0.757 5.666 3.548 0.00 0.00 H
ATOM 183 H X 1 -0.757 5.666 3.548 0.00 0.00 H
ATOM 184 O X 1 0.000 5.187 10.545 0.00 0.00 O
ATOM 185 H X 1 0.757 5.666 10.883 0.00 0.00 H
ATOM 186 H X 1 -0.757 5.666 10.883 0.00 0.00 H
ATOM 187 O X 1 0.000 12.968 3.209 0.00 0.00 O
ATOM 188 H X 1 0.757 13.447 3.548 0.00 0.00 H
ATOM 189 H X 1 -0.757 13.447 3.548 0.00 0.00 H
ATOM 190 O X 1 0.000 12.968 10.545 0.00 0.00 O
ATOM 191 H X 1 0.757 13.447 10.883 0.00 0.00 H
ATOM 192 H X 1 -0.757 13.447 10.883 0.00 0.00 H
ATOM 193 O X 1 4.492 5.187 3.209 0.00 0.00 O
ATOM 194 H X 1 5.249 5.666 3.548 0.00 0.00 H
ATOM 195 H X 1 3.735 5.666 3.548 0.00 0.00 H
ATOM 196 O X 1 4.492 5.187 10.545 0.00 0.00 O
ATOM 197 H X 1 5.249 5.666 10.883 0.00 0.00 H
ATOM 198 H X 1 3.735 5.666 10.883 0.00 0.00 H
ATOM 199 O X 1 4.492 12.968 3.209 0.00 0.00 O
ATOM 200 H X 1 5.249 13.447 3.548 0.00 0.00 H
ATOM 201 H X 1 3.735 13.447 3.548 0.00 0.00 H
ATOM 202 O X 1 4.492 12.968 10.545 0.00 0.00 O
ATOM 203 H X 1 5.249 13.447 10.883 0.00 0.00 H
ATOM 204 H X 1 3.735 13.447 10.883 0.00 0.00 H
ATOM 205 O X 1 8.984 5.187 3.209 0.00 0.00 O
ATOM 206 H X 1 9.741 5.666 3.548 0.00 0.00 H
ATOM 207 H X 1 8.228 5.666 3.548 0.00 0.00 H
ATOM 208 O X 1 8.984 5.187 10.545 0.00 0.00 O
ATOM 209 H X 1 9.741 5.666 10.883 0.00 0.00 H
ATOM 210 H X 1 8.228 5.666 10.883 0.00 0.00 H
ATOM 211 O X 1 8.984 12.968 3.209 0.00 0.00 O
ATOM 212 H X 1 9.741 13.447 3.548 0.00 0.00 H
ATOM 213 H X 1 8.228 13.447 3.548 0.00 0.00 H
ATOM 214 O X 1 8.984 12.968 10.545 0.00 0.00 O
ATOM 215 H X 1 9.741 13.447 10.883 0.00 0.00 H
ATOM 216 H X 1 8.228 13.447 10.883 0.00 0.00 H
ATOM 217 O X 1 2.246 6.484 6.877 0.00 0.00 O
ATOM 218 H X 1 1.489 6.005 7.215 0.00 0.00 H
ATOM 219 H X 1 3.003 6.005 7.215 0.00 0.00 H
ATOM 220 O X 1 2.246 6.484 14.213 0.00 0.00 O
ATOM 221 H X 1 1.489 6.005 14.551 0.00 0.00 H
ATOM 222 H X 1 3.003 6.005 14.551 0.00 0.00 H
ATOM 223 O X 1 2.246 14.265 6.877 0.00 0.00 O
ATOM 224 H X 1 1.489 13.786 7.215 0.00 0.00 H
ATOM 225 H X 1 3.003 13.786 7.215 0.00 0.00 H
ATOM 226 O X 1 2.246 14.265 14.213 0.00 0.00 O
ATOM 227 H X 1 1.489 13.786 14.551 0.00 0.00 H
ATOM 228 H X 1 3.003 13.786 14.551 0.00 0.00 H
ATOM 229 O X 1 6.738 6.484 6.877 0.00 0.00 O
ATOM 230 H X 1 5.981 6.005 7.215 0.00 0.00 H
ATOM 231 H X 1 7.495 6.005 7.215 0.00 0.00 H
ATOM 232 O X 1 6.738 6.484 14.213 0.00 0.00 O
ATOM 233 H X 1 5.981 6.005 14.551 0.00 0.00 H
ATOM 234 H X 1 7.495 6.005 14.551 0.00 0.00 H
ATOM 235 O X 1 6.738 14.265 6.877 0.00 0.00 O
ATOM 236 H X 1 5.981 13.786 7.215 0.00 0.00 H
ATOM 237 H X 1 7.495 13.786 7.215 0.00 0.00 H
ATOM 238 O X 1 6.738 14.265 14.213 0.00 0.00 O
ATOM 239 H X 1 5.981 13.786 14.551 0.00 0.00 H
ATOM 240 H X 1 7.495 13.786 14.551 0.00 0.00 H
ATOM 241 O X 1 11.231 6.484 6.877 0.00 0.00 O
ATOM 242 H X 1 10.474 6.005 7.215 0.00 0.00 H
ATOM 243 H X 1 11.988 6.005 7.215 0.00 0.00 H
ATOM 244 O X 1 11.231 6.484 14.213 0.00 0.00 O
ATOM 245 H X 1 10.474 6.005 14.551 0.00 0.00 H
ATOM 246 H X 1 11.988 6.005 14.551 0.00 0.00 H
ATOM 247 O X 1 11.231 14.265 6.877 0.00 0.00 O
ATOM 248 H X 1 10.474 13.786 7.215 0.00 0.00 H
ATOM 249 H X 1 11.988 13.786 7.215 0.00 0.00 H
ATOM 250 O X 1 11.231 14.265 14.213 0.00 0.00 O
ATOM 251 H X 1 10.474 13.786 14.551 0.00 0.00 H
ATOM 252 H X 1 11.988 13.786 14.551 0.00 0.00 H
ATOM 253 O X 1 0.000 2.593 6.877 0.00 0.00 O
ATOM 254 H X 1 -0.757 2.115 7.215 0.00 0.00 H
ATOM 255 H X 1 0.757 2.115 7.215 0.00 0.00 H
ATOM 256 O X 1 0.000 2.593 14.213 0.00 0.00 O
ATOM 257 H X 1 -0.757 2.115 14.551 0.00 0.00 H
ATOM 258 H X 1 0.757 2.115 14.551 0.00 0.00 H
ATOM 259 O X 1 0.000 10.374 6.877 0.00 0.00 O
ATOM 260 H X 1 -0.757 9.896 7.215 0.00 0.00 H
ATOM 261 H X 1 0.757 9.896 7.215 0.00 0.00 H
ATOM 262 O X 1 0.000 10.374 14.213 0.00 0.00 O
ATOM 263 H X 1 -0.757 9.896 14.551 0.00 0.00 H
ATOM 264 H X 1 0.757 9.896 14.551 0.00 0.00 H
ATOM 265 O X 1 4.492 2.593 6.877 0.00 0.00 O
ATOM 266 H X 1 3.735 2.115 7.215 0.00 0.00 H
ATOM 267 H X 1 5.249 2.115 7.215 0.00 0.00 H
ATOM 268 O X 1 4.492 2.593 14.213 0.00 0.00 O
ATOM 269 H X 1 3.735 2.115 14.551 0.00 0.00 H
ATOM 270 H X 1 5.249 2.115 14.551 0.00 0.00 H
ATOM 271 O X 1 4.492 10.374 6.877 0.00 0.00 O
ATOM 272 H X 1 3.735 9.896 7.215 0.00 0.00 H
ATOM 273 H X 1 5.249 9.896 7.215 0.00 0.00 H
ATOM 274 O X 1 4.492 10.374 14.213 0.00 0.00 O
ATOM 275 H X 1 3.735 9.896 14.551 0.00 0.00 H
ATOM 276 H X 1 5.249 9.896 14.551 0.00 0.00 H
ATOM 277 O X 1 8.984 2.593 6.877 0.00 0.00 O
ATOM 278 H X 1 8.228 2.115 7.215 0.00 0.00 H
ATOM 279 H X 1 9.741 2.115 7.215 0.00 0.00 H
ATOM 280 O X 1 8.984 2.593 14.213 0.00 0.00 O
ATOM 281 H X 1 8.228 2.115 14.551 0.00 0.00 H
ATOM 282 H X 1 9.741 2.115 14.551 0.00 0.00 H
ATOM 283 O X 1 8.984 10.374 6.877 0.00 0.00 O
ATOM 284 H X 1 8.228 9.896 7.215 0.00 0.00 H
ATOM 285 H X 1 9.741 9.896 7.215 0.00 0.00 H
ATOM 286 O X 1 8.984 10.374 14.213 0.00 0.00 O
ATOM 287 H X 1 8.228 9.896 14.551 0.00 0.00 H
ATOM 288 H X 1 9.741 9.896 14.551 0.00 0.00 H
END
...
es: 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=1-384
SIGMA the width to use for the gaussian kernels=0.05
CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
REFERENCEPDB files with relative distances from central atom= ATOM 1 O MOL 1 -2.239 -1.296 -0.917 1.00 0.00 O
ATOM 2 O MOL 1 0.000 0.000 2.751 1.00 0.00 O
ATOM 3 O MOL 1 0.000 2.594 -0.917 1.00 0.00 O
ATOM 4 O MOL 1 2.246 -1.296 -0.917 1.00 0.00 O
MEAN calculate the mean of all the quantities
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.={RATIONAL R_0=0.5 NN=12 MM=24}
ATOM_NAMES_FILEPDB file with atom names for all atoms in SPECIES= CRYST1 13.470 15.562 14.672 90.00 90.00 90.00 P 1 1
ATOM 1 O X 1 0.000 2.593 4.126 0.00 0.00 O
ATOM 4 O X 1 0.000 2.593 11.462 0.00 0.00 O
ATOM 7 O X 1 0.000 10.374 4.126 0.00 0.00 O
ATOM 10 O X 1 0.000 10.374 11.462 0.00 0.00 O
ATOM 13 O X 1 4.492 2.593 4.126 0.00 0.00 O
ATOM 16 O X 1 4.492 2.593 11.462 0.00 0.00 O
ATOM 19 O X 1 4.492 10.374 4.126 0.00 0.00 O
ATOM 22 O X 1 4.492 10.374 11.462 0.00 0.00 O
ATOM 25 O X 1 8.984 2.593 4.126 0.00 0.00 O
ATOM 28 O X 1 8.984 2.593 11.462 0.00 0.00 O
ATOM 31 O X 1 8.984 10.374 4.126 0.00 0.00 O
ATOM 34 O X 1 8.984 10.374 11.462 0.00 0.00 O
ATOM 37 O X 1 2.246 6.484 4.126 0.00 0.00 O
ATOM 40 O X 1 2.246 6.484 11.462 0.00 0.00 O
ATOM 43 O X 1 2.246 14.265 4.126 0.00 0.00 O
ATOM 46 O X 1 2.246 14.265 11.462 0.00 0.00 O
ATOM 49 O X 1 6.738 6.484 4.126 0.00 0.00 O
ATOM 52 O X 1 6.738 6.484 11.462 0.00 0.00 O
ATOM 55 O X 1 6.738 14.265 4.126 0.00 0.00 O
ATOM 58 O X 1 6.738 14.265 11.462 0.00 0.00 O
ATOM 61 O X 1 11.231 6.484 4.126 0.00 0.00 O
ATOM 64 O X 1 11.231 6.484 11.462 0.00 0.00 O
ATOM 67 O X 1 11.231 14.265 4.126 0.00 0.00 O
ATOM 70 O X 1 11.231 14.265 11.462 0.00 0.00 O
ATOM 73 O X 1 0.000 5.187 7.794 0.00 0.00 O
ATOM 76 O X 1 0.000 5.187 15.130 0.00 0.00 O
ATOM 79 O X 1 0.000 12.968 7.794 0.00 0.00 O
ATOM 82 O X 1 0.000 12.968 15.130 0.00 0.00 O
ATOM 85 O X 1 4.492 5.187 7.794 0.00 0.00 O
ATOM 88 O X 1 4.492 5.187 15.130 0.00 0.00 O
ATOM 91 O X 1 4.492 12.968 7.794 0.00 0.00 O
ATOM 94 O X 1 4.492 12.968 15.130 0.00 0.00 O
ATOM 97 O X 1 8.984 5.187 7.794 0.00 0.00 O
ATOM 100 O X 1 8.984 5.187 15.130 0.00 0.00 O
ATOM 103 O X 1 8.984 12.968 7.794 0.00 0.00 O
ATOM 106 O X 1 8.984 12.968 15.130 0.00 0.00 O
ATOM 109 O X 1 2.246 1.297 7.794 0.00 0.00 O
ATOM 112 O X 1 2.246 1.297 15.130 0.00 0.00 O
ATOM 115 O X 1 2.246 9.078 7.794 0.00 0.00 O
ATOM 118 O X 1 2.246 9.078 15.130 0.00 0.00 O
ATOM 121 O X 1 6.738 1.297 7.794 0.00 0.00 O
ATOM 124 O X 1 6.738 1.297 15.130 0.00 0.00 O
ATOM 127 O X 1 6.738 9.078 7.794 0.00 0.00 O
ATOM 130 O X 1 6.738 9.078 15.130 0.00 0.00 O
ATOM 133 O X 1 11.231 1.297 7.794 0.00 0.00 O
ATOM 136 O X 1 11.231 1.297 15.130 0.00 0.00 O
ATOM 139 O X 1 11.231 9.078 7.794 0.00 0.00 O
ATOM 142 O X 1 11.231 9.078 15.130 0.00 0.00 O
ATOM 145 O X 1 2.246 1.297 3.209 0.00 0.00 O
ATOM 148 O X 1 2.246 1.297 10.545 0.00 0.00 O
ATOM 151 O X 1 2.246 9.078 3.209 0.00 0.00 O
ATOM 154 O X 1 2.246 9.078 10.545 0.00 0.00 O
ATOM 157 O X 1 6.738 1.297 3.209 0.00 0.00 O
ATOM 160 O X 1 6.738 1.297 10.545 0.00 0.00 O
ATOM 163 O X 1 6.738 9.078 3.209 0.00 0.00 O
ATOM 166 O X 1 6.738 9.078 10.545 0.00 0.00 O
ATOM 169 O X 1 11.231 1.297 3.209 0.00 0.00 O
ATOM 172 O X 1 11.231 1.297 10.545 0.00 0.00 O
ATOM 175 O X 1 11.231 9.078 3.209 0.00 0.00 O
ATOM 178 O X 1 11.231 9.078 10.545 0.00 0.00 O
ATOM 181 O X 1 0.000 5.187 3.209 0.00 0.00 O
ATOM 184 O X 1 0.000 5.187 10.545 0.00 0.00 O
ATOM 187 O X 1 0.000 12.968 3.209 0.00 0.00 O
ATOM 190 O X 1 0.000 12.968 10.545 0.00 0.00 O
ATOM 193 O X 1 4.492 5.187 3.209 0.00 0.00 O
ATOM 196 O X 1 4.492 5.187 10.545 0.00 0.00 O
ATOM 199 O X 1 4.492 12.968 3.209 0.00 0.00 O
ATOM 202 O X 1 4.492 12.968 10.545 0.00 0.00 O
ATOM 205 O X 1 8.984 5.187 3.209 0.00 0.00 O
ATOM 208 O X 1 8.984 5.187 10.545 0.00 0.00 O
ATOM 211 O X 1 8.984 12.968 3.209 0.00 0.00 O
ATOM 214 O X 1 8.984 12.968 10.545 0.00 0.00 O
ATOM 217 O X 1 2.246 6.484 6.877 0.00 0.00 O
ATOM 220 O X 1 2.246 6.484 14.213 0.00 0.00 O
ATOM 223 O X 1 2.246 14.265 6.877 0.00 0.00 O
ATOM 226 O X 1 2.246 14.265 14.213 0.00 0.00 O
ATOM 229 O X 1 6.738 6.484 6.877 0.00 0.00 O
ATOM 232 O X 1 6.738 6.484 14.213 0.00 0.00 O
ATOM 235 O X 1 6.738 14.265 6.877 0.00 0.00 O
ATOM 238 O X 1 6.738 14.265 14.213 0.00 0.00 O
ATOM 241 O X 1 11.231 6.484 6.877 0.00 0.00 O
ATOM 244 O X 1 11.231 6.484 14.213 0.00 0.00 O
ATOM 247 O X 1 11.231 14.265 6.877 0.00 0.00 O
ATOM 250 O X 1 11.231 14.265 14.213 0.00 0.00 O
ATOM 253 O X 1 0.000 2.593 6.877 0.00 0.00 O
ATOM 256 O X 1 0.000 2.593 14.213 0.00 0.00 O
ATOM 259 O X 1 0.000 10.374 6.877 0.00 0.00 O
ATOM 262 O X 1 0.000 10.374 14.213 0.00 0.00 O
ATOM 265 O X 1 4.492 2.593 6.877 0.00 0.00 O
ATOM 268 O X 1 4.492 2.593 14.213 0.00 0.00 O
ATOM 271 O X 1 4.492 10.374 6.877 0.00 0.00 O
ATOM 274 O X 1 4.492 10.374 14.213 0.00 0.00 O
ATOM 277 O X 1 8.984 2.593 6.877 0.00 0.00 O
ATOM 280 O X 1 8.984 2.593 14.213 0.00 0.00 O
ATOM 283 O X 1 8.984 10.374 6.877 0.00 0.00 O
ATOM 286 O X 1 8.984 10.374 14.213 0.00 0.00 O
ATOM 1 O X 1 0.000 2.593 4.126 0.00 0.00 O
ATOM 2 H X 1 0.000 3.509 3.847 0.00 0.00 H
ATOM 3 H X 1 0.000 2.635 5.083 0.00 0.00 H
ATOM 4 O X 1 0.000 2.593 11.462 0.00 0.00 O
ATOM 5 H X 1 0.000 3.509 11.183 0.00 0.00 H
ATOM 6 H X 1 0.000 2.635 12.419 0.00 0.00 H
ATOM 7 O X 1 0.000 10.374 4.126 0.00 0.00 O
ATOM 8 H X 1 0.000 11.290 3.847 0.00 0.00 H
ATOM 9 H X 1 0.000 10.415 5.083 0.00 0.00 H
ATOM 10 O X 1 0.000 10.374 11.462 0.00 0.00 O
ATOM 11 H X 1 0.000 11.290 11.183 0.00 0.00 H
ATOM 12 H X 1 0.000 10.415 12.419 0.00 0.00 H
ATOM 13 O X 1 4.492 2.593 4.126 0.00 0.00 O
ATOM 14 H X 1 4.492 3.509 3.847 0.00 0.00 H
ATOM 15 H X 1 4.492 2.635 5.083 0.00 0.00 H
ATOM 16 O X 1 4.492 2.593 11.462 0.00 0.00 O
ATOM 17 H X 1 4.492 3.509 11.183 0.00 0.00 H
ATOM 18 H X 1 4.492 2.635 12.419 0.00 0.00 H
ATOM 19 O X 1 4.492 10.374 4.126 0.00 0.00 O
ATOM 20 H X 1 4.492 11.290 3.847 0.00 0.00 H
ATOM 21 H X 1 4.492 10.415 5.083 0.00 0.00 H
ATOM 22 O X 1 4.492 10.374 11.462 0.00 0.00 O
ATOM 23 H X 1 4.492 11.290 11.183 0.00 0.00 H
ATOM 24 H X 1 4.492 10.415 12.419 0.00 0.00 H
ATOM 25 O X 1 8.984 2.593 4.126 0.00 0.00 O
ATOM 26 H X 1 8.984 3.509 3.847 0.00 0.00 H
ATOM 27 H X 1 8.984 2.635 5.083 0.00 0.00 H
ATOM 28 O X 1 8.984 2.593 11.462 0.00 0.00 O
ATOM 29 H X 1 8.984 3.509 11.183 0.00 0.00 H
ATOM 30 H X 1 8.984 2.635 12.419 0.00 0.00 H
ATOM 31 O X 1 8.984 10.374 4.126 0.00 0.00 O
ATOM 32 H X 1 8.984 11.290 3.847 0.00 0.00 H
ATOM 33 H X 1 8.984 10.415 5.083 0.00 0.00 H
ATOM 34 O X 1 8.984 10.374 11.462 0.00 0.00 O
ATOM 35 H X 1 8.984 11.290 11.183 0.00 0.00 H
ATOM 36 H X 1 8.984 10.415 12.419 0.00 0.00 H
ATOM 37 O X 1 2.246 6.484 4.126 0.00 0.00 O
ATOM 38 H X 1 2.246 7.400 3.847 0.00 0.00 H
ATOM 39 H X 1 2.246 6.525 5.083 0.00 0.00 H
ATOM 40 O X 1 2.246 6.484 11.462 0.00 0.00 O
ATOM 41 H X 1 2.246 7.400 11.183 0.00 0.00 H
ATOM 42 H X 1 2.246 6.525 12.419 0.00 0.00 H
ATOM 43 O X 1 2.246 14.265 4.126 0.00 0.00 O
ATOM 44 H X 1 2.246 15.180 3.847 0.00 0.00 H
ATOM 45 H X 1 2.246 14.306 5.083 0.00 0.00 H
ATOM 46 O X 1 2.246 14.265 11.462 0.00 0.00 O
ATOM 47 H X 1 2.246 15.180 11.183 0.00 0.00 H
ATOM 48 H X 1 2.246 14.306 12.419 0.00 0.00 H
ATOM 49 O X 1 6.738 6.484 4.126 0.00 0.00 O
ATOM 50 H X 1 6.738 7.400 3.847 0.00 0.00 H
ATOM 51 H X 1 6.738 6.525 5.083 0.00 0.00 H
ATOM 52 O X 1 6.738 6.484 11.462 0.00 0.00 O
ATOM 53 H X 1 6.738 7.400 11.183 0.00 0.00 H
ATOM 54 H X 1 6.738 6.525 12.419 0.00 0.00 H
ATOM 55 O X 1 6.738 14.265 4.126 0.00 0.00 O
ATOM 56 H X 1 6.738 15.180 3.847 0.00 0.00 H
ATOM 57 H X 1 6.738 14.306 5.083 0.00 0.00 H
ATOM 58 O X 1 6.738 14.265 11.462 0.00 0.00 O
ATOM 59 H X 1 6.738 15.180 11.183 0.00 0.00 H
ATOM 60 H X 1 6.738 14.306 12.419 0.00 0.00 H
ATOM 61 O X 1 11.231 6.484 4.126 0.00 0.00 O
ATOM 62 H X 1 11.231 7.400 3.847 0.00 0.00 H
ATOM 63 H X 1 11.231 6.525 5.083 0.00 0.00 H
ATOM 64 O X 1 11.231 6.484 11.462 0.00 0.00 O
ATOM 65 H X 1 11.231 7.400 11.183 0.00 0.00 H
ATOM 66 H X 1 11.231 6.525 12.419 0.00 0.00 H
ATOM 67 O X 1 11.231 14.265 4.126 0.00 0.00 O
ATOM 68 H X 1 11.231 15.180 3.847 0.00 0.00 H
ATOM 69 H X 1 11.231 14.306 5.083 0.00 0.00 H
ATOM 70 O X 1 11.231 14.265 11.462 0.00 0.00 O
ATOM 71 H X 1 11.231 15.180 11.183 0.00 0.00 H
ATOM 72 H X 1 11.231 14.306 12.419 0.00 0.00 H
ATOM 73 O X 1 0.000 5.187 7.794 0.00 0.00 O
ATOM 74 H X 1 0.000 4.272 7.515 0.00 0.00 H
ATOM 75 H X 1 0.000 5.146 8.751 0.00 0.00 H
ATOM 76 O X 1 0.000 5.187 15.130 0.00 0.00 O
ATOM 77 H X 1 0.000 4.272 14.851 0.00 0.00 H
ATOM 78 H X 1 0.000 5.146 16.087 0.00 0.00 H
ATOM 79 O X 1 0.000 12.968 7.794 0.00 0.00 O
ATOM 80 H X 1 0.000 12.052 7.515 0.00 0.00 H
ATOM 81 H X 1 0.000 12.927 8.751 0.00 0.00 H
ATOM 82 O X 1 0.000 12.968 15.130 0.00 0.00 O
ATOM 83 H X 1 0.000 12.052 14.851 0.00 0.00 H
ATOM 84 H X 1 0.000 12.927 16.087 0.00 0.00 H
ATOM 85 O X 1 4.492 5.187 7.794 0.00 0.00 O
ATOM 86 H X 1 4.492 4.272 7.515 0.00 0.00 H
ATOM 87 H X 1 4.492 5.146 8.751 0.00 0.00 H
ATOM 88 O X 1 4.492 5.187 15.130 0.00 0.00 O
ATOM 89 H X 1 4.492 4.272 14.851 0.00 0.00 H
ATOM 90 H X 1 4.492 5.146 16.087 0.00 0.00 H
ATOM 91 O X 1 4.492 12.968 7.794 0.00 0.00 O
ATOM 92 H X 1 4.492 12.052 7.515 0.00 0.00 H
ATOM 93 H X 1 4.492 12.927 8.751 0.00 0.00 H
ATOM 94 O X 1 4.492 12.968 15.130 0.00 0.00 O
ATOM 95 H X 1 4.492 12.052 14.851 0.00 0.00 H
ATOM 96 H X 1 4.492 12.927 16.087 0.00 0.00 H
ATOM 97 O X 1 8.984 5.187 7.794 0.00 0.00 O
ATOM 98 H X 1 8.984 4.272 7.515 0.00 0.00 H
ATOM 99 H X 1 8.984 5.146 8.751 0.00 0.00 H
ATOM 100 O X 1 8.984 5.187 15.130 0.00 0.00 O
ATOM 101 H X 1 8.984 4.272 14.851 0.00 0.00 H
ATOM 102 H X 1 8.984 5.146 16.087 0.00 0.00 H
ATOM 103 O X 1 8.984 12.968 7.794 0.00 0.00 O
ATOM 104 H X 1 8.984 12.052 7.515 0.00 0.00 H
ATOM 105 H X 1 8.984 12.927 8.751 0.00 0.00 H
ATOM 106 O X 1 8.984 12.968 15.130 0.00 0.00 O
ATOM 107 H X 1 8.984 12.052 14.851 0.00 0.00 H
ATOM 108 H X 1 8.984 12.927 16.087 0.00 0.00 H
ATOM 109 O X 1 2.246 1.297 7.794 0.00 0.00 O
ATOM 110 H X 1 2.246 0.381 7.515 0.00 0.00 H
ATOM 111 H X 1 2.246 1.256 8.751 0.00 0.00 H
ATOM 112 O X 1 2.246 1.297 15.130 0.00 0.00 O
ATOM 113 H X 1 2.246 0.381 14.851 0.00 0.00 H
ATOM 114 H X 1 2.246 1.256 16.087 0.00 0.00 H
ATOM 115 O X 1 2.246 9.078 7.794 0.00 0.00 O
ATOM 116 H X 1 2.246 8.162 7.515 0.00 0.00 H
ATOM 117 H X 1 2.246 9.037 8.751 0.00 0.00 H
ATOM 118 O X 1 2.246 9.078 15.130 0.00 0.00 O
ATOM 119 H X 1 2.246 8.162 14.851 0.00 0.00 H
ATOM 120 H X 1 2.246 9.037 16.087 0.00 0.00 H
ATOM 121 O X 1 6.738 1.297 7.794 0.00 0.00 O
ATOM 122 H X 1 6.738 0.381 7.515 0.00 0.00 H
ATOM 123 H X 1 6.738 1.256 8.751 0.00 0.00 H
ATOM 124 O X 1 6.738 1.297 15.130 0.00 0.00 O
ATOM 125 H X 1 6.738 0.381 14.851 0.00 0.00 H
ATOM 126 H X 1 6.738 1.256 16.087 0.00 0.00 H
ATOM 127 O X 1 6.738 9.078 7.794 0.00 0.00 O
ATOM 128 H X 1 6.738 8.162 7.515 0.00 0.00 H
ATOM 129 H X 1 6.738 9.037 8.751 0.00 0.00 H
ATOM 130 O X 1 6.738 9.078 15.130 0.00 0.00 O
ATOM 131 H X 1 6.738 8.162 14.851 0.00 0.00 H
ATOM 132 H X 1 6.738 9.037 16.087 0.00 0.00 H
ATOM 133 O X 1 11.231 1.297 7.794 0.00 0.00 O
ATOM 134 H X 1 11.231 0.381 7.515 0.00 0.00 H
ATOM 135 H X 1 11.231 1.256 8.751 0.00 0.00 H
ATOM 136 O X 1 11.231 1.297 15.130 0.00 0.00 O
ATOM 137 H X 1 11.231 0.381 14.851 0.00 0.00 H
ATOM 138 H X 1 11.231 1.256 16.087 0.00 0.00 H
ATOM 139 O X 1 11.231 9.078 7.794 0.00 0.00 O
ATOM 140 H X 1 11.231 8.162 7.515 0.00 0.00 H
ATOM 141 H X 1 11.231 9.037 8.751 0.00 0.00 H
ATOM 142 O X 1 11.231 9.078 15.130 0.00 0.00 O
ATOM 143 H X 1 11.231 8.162 14.851 0.00 0.00 H
ATOM 144 H X 1 11.231 9.037 16.087 0.00 0.00 H
ATOM 145 O X 1 2.246 1.297 3.209 0.00 0.00 O
ATOM 146 H X 1 3.003 1.776 3.548 0.00 0.00 H
ATOM 147 H X 1 1.489 1.776 3.548 0.00 0.00 H
ATOM 148 O X 1 2.246 1.297 10.545 0.00 0.00 O
ATOM 149 H X 1 3.003 1.776 10.883 0.00 0.00 H
ATOM 150 H X 1 1.489 1.776 10.883 0.00 0.00 H
ATOM 151 O X 1 2.246 9.078 3.209 0.00 0.00 O
ATOM 152 H X 1 3.003 9.556 3.548 0.00 0.00 H
ATOM 153 H X 1 1.489 9.556 3.548 0.00 0.00 H
ATOM 154 O X 1 2.246 9.078 10.545 0.00 0.00 O
ATOM 155 H X 1 3.003 9.556 10.883 0.00 0.00 H
ATOM 156 H X 1 1.489 9.556 10.883 0.00 0.00 H
ATOM 157 O X 1 6.738 1.297 3.209 0.00 0.00 O
ATOM 158 H X 1 7.495 1.776 3.548 0.00 0.00 H
ATOM 159 H X 1 5.981 1.776 3.548 0.00 0.00 H
ATOM 160 O X 1 6.738 1.297 10.545 0.00 0.00 O
ATOM 161 H X 1 7.495 1.776 10.883 0.00 0.00 H
ATOM 162 H X 1 5.981 1.776 10.883 0.00 0.00 H
ATOM 163 O X 1 6.738 9.078 3.209 0.00 0.00 O
ATOM 164 H X 1 7.495 9.556 3.548 0.00 0.00 H
ATOM 165 H X 1 5.981 9.556 3.548 0.00 0.00 H
ATOM 166 O X 1 6.738 9.078 10.545 0.00 0.00 O
ATOM 167 H X 1 7.495 9.556 10.883 0.00 0.00 H
ATOM 168 H X 1 5.981 9.556 10.883 0.00 0.00 H
ATOM 169 O X 1 11.231 1.297 3.209 0.00 0.00 O
ATOM 170 H X 1 11.988 1.776 3.548 0.00 0.00 H
ATOM 171 H X 1 10.474 1.776 3.548 0.00 0.00 H
ATOM 172 O X 1 11.231 1.297 10.545 0.00 0.00 O
ATOM 173 H X 1 11.988 1.776 10.883 0.00 0.00 H
ATOM 174 H X 1 10.474 1.776 10.883 0.00 0.00 H
ATOM 175 O X 1 11.231 9.078 3.209 0.00 0.00 O
ATOM 176 H X 1 11.988 9.556 3.548 0.00 0.00 H
ATOM 177 H X 1 10.474 9.556 3.548 0.00 0.00 H
ATOM 178 O X 1 11.231 9.078 10.545 0.00 0.00 O
ATOM 179 H X 1 11.988 9.556 10.883 0.00 0.00 H
ATOM 180 H X 1 10.474 9.556 10.883 0.00 0.00 H
ATOM 181 O X 1 0.000 5.187 3.209 0.00 0.00 O
ATOM 182 H X 1 0.757 5.666 3.548 0.00 0.00 H
ATOM 183 H X 1 -0.757 5.666 3.548 0.00 0.00 H
ATOM 184 O X 1 0.000 5.187 10.545 0.00 0.00 O
ATOM 185 H X 1 0.757 5.666 10.883 0.00 0.00 H
ATOM 186 H X 1 -0.757 5.666 10.883 0.00 0.00 H
ATOM 187 O X 1 0.000 12.968 3.209 0.00 0.00 O
ATOM 188 H X 1 0.757 13.447 3.548 0.00 0.00 H
ATOM 189 H X 1 -0.757 13.447 3.548 0.00 0.00 H
ATOM 190 O X 1 0.000 12.968 10.545 0.00 0.00 O
ATOM 191 H X 1 0.757 13.447 10.883 0.00 0.00 H
ATOM 192 H X 1 -0.757 13.447 10.883 0.00 0.00 H
ATOM 193 O X 1 4.492 5.187 3.209 0.00 0.00 O
ATOM 194 H X 1 5.249 5.666 3.548 0.00 0.00 H
ATOM 195 H X 1 3.735 5.666 3.548 0.00 0.00 H
ATOM 196 O X 1 4.492 5.187 10.545 0.00 0.00 O
ATOM 197 H X 1 5.249 5.666 10.883 0.00 0.00 H
ATOM 198 H X 1 3.735 5.666 10.883 0.00 0.00 H
ATOM 199 O X 1 4.492 12.968 3.209 0.00 0.00 O
ATOM 200 H X 1 5.249 13.447 3.548 0.00 0.00 H
ATOM 201 H X 1 3.735 13.447 3.548 0.00 0.00 H
ATOM 202 O X 1 4.492 12.968 10.545 0.00 0.00 O
ATOM 203 H X 1 5.249 13.447 10.883 0.00 0.00 H
ATOM 204 H X 1 3.735 13.447 10.883 0.00 0.00 H
ATOM 205 O X 1 8.984 5.187 3.209 0.00 0.00 O
ATOM 206 H X 1 9.741 5.666 3.548 0.00 0.00 H
ATOM 207 H X 1 8.228 5.666 3.548 0.00 0.00 H
ATOM 208 O X 1 8.984 5.187 10.545 0.00 0.00 O
ATOM 209 H X 1 9.741 5.666 10.883 0.00 0.00 H
ATOM 210 H X 1 8.228 5.666 10.883 0.00 0.00 H
ATOM 211 O X 1 8.984 12.968 3.209 0.00 0.00 O
ATOM 212 H X 1 9.741 13.447 3.548 0.00 0.00 H
ATOM 213 H X 1 8.228 13.447 3.548 0.00 0.00 H
ATOM 214 O X 1 8.984 12.968 10.545 0.00 0.00 O
ATOM 215 H X 1 9.741 13.447 10.883 0.00 0.00 H
ATOM 216 H X 1 8.228 13.447 10.883 0.00 0.00 H
ATOM 217 O X 1 2.246 6.484 6.877 0.00 0.00 O
ATOM 218 H X 1 1.489 6.005 7.215 0.00 0.00 H
ATOM 219 H X 1 3.003 6.005 7.215 0.00 0.00 H
ATOM 220 O X 1 2.246 6.484 14.213 0.00 0.00 O
ATOM 221 H X 1 1.489 6.005 14.551 0.00 0.00 H
ATOM 222 H X 1 3.003 6.005 14.551 0.00 0.00 H
ATOM 223 O X 1 2.246 14.265 6.877 0.00 0.00 O
ATOM 224 H X 1 1.489 13.786 7.215 0.00 0.00 H
ATOM 225 H X 1 3.003 13.786 7.215 0.00 0.00 H
ATOM 226 O X 1 2.246 14.265 14.213 0.00 0.00 O
ATOM 227 H X 1 1.489 13.786 14.551 0.00 0.00 H
ATOM 228 H X 1 3.003 13.786 14.551 0.00 0.00 H
ATOM 229 O X 1 6.738 6.484 6.877 0.00 0.00 O
ATOM 230 H X 1 5.981 6.005 7.215 0.00 0.00 H
ATOM 231 H X 1 7.495 6.005 7.215 0.00 0.00 H
ATOM 232 O X 1 6.738 6.484 14.213 0.00 0.00 O
ATOM 233 H X 1 5.981 6.005 14.551 0.00 0.00 H
ATOM 234 H X 1 7.495 6.005 14.551 0.00 0.00 H
ATOM 235 O X 1 6.738 14.265 6.877 0.00 0.00 O
ATOM 236 H X 1 5.981 13.786 7.215 0.00 0.00 H
ATOM 237 H X 1 7.495 13.786 7.215 0.00 0.00 H
ATOM 238 O X 1 6.738 14.265 14.213 0.00 0.00 O
ATOM 239 H X 1 5.981 13.786 14.551 0.00 0.00 H
ATOM 240 H X 1 7.495 13.786 14.551 0.00 0.00 H
ATOM 241 O X 1 11.231 6.484 6.877 0.00 0.00 O
ATOM 242 H X 1 10.474 6.005 7.215 0.00 0.00 H
ATOM 243 H X 1 11.988 6.005 7.215 0.00 0.00 H
ATOM 244 O X 1 11.231 6.484 14.213 0.00 0.00 O
ATOM 245 H X 1 10.474 6.005 14.551 0.00 0.00 H
ATOM 246 H X 1 11.988 6.005 14.551 0.00 0.00 H
ATOM 247 O X 1 11.231 14.265 6.877 0.00 0.00 O
ATOM 248 H X 1 10.474 13.786 7.215 0.00 0.00 H
ATOM 249 H X 1 11.988 13.786 7.215 0.00 0.00 H
ATOM 250 O X 1 11.231 14.265 14.213 0.00 0.00 O
ATOM 251 H X 1 10.474 13.786 14.551 0.00 0.00 H
ATOM 252 H X 1 11.988 13.786 14.551 0.00 0.00 H
ATOM 253 O X 1 0.000 2.593 6.877 0.00 0.00 O
ATOM 254 H X 1 -0.757 2.115 7.215 0.00 0.00 H
ATOM 255 H X 1 0.757 2.115 7.215 0.00 0.00 H
ATOM 256 O X 1 0.000 2.593 14.213 0.00 0.00 O
ATOM 257 H X 1 -0.757 2.115 14.551 0.00 0.00 H
ATOM 258 H X 1 0.757 2.115 14.551 0.00 0.00 H
ATOM 259 O X 1 0.000 10.374 6.877 0.00 0.00 O
ATOM 260 H X 1 -0.757 9.896 7.215 0.00 0.00 H
ATOM 261 H X 1 0.757 9.896 7.215 0.00 0.00 H
ATOM 262 O X 1 0.000 10.374 14.213 0.00 0.00 O
ATOM 263 H X 1 -0.757 9.896 14.551 0.00 0.00 H
ATOM 264 H X 1 0.757 9.896 14.551 0.00 0.00 H
ATOM 265 O X 1 4.492 2.593 6.877 0.00 0.00 O
ATOM 266 H X 1 3.735 2.115 7.215 0.00 0.00 H
ATOM 267 H X 1 5.249 2.115 7.215 0.00 0.00 H
ATOM 268 O X 1 4.492 2.593 14.213 0.00 0.00 O
ATOM 269 H X 1 3.735 2.115 14.551 0.00 0.00 H
ATOM 270 H X 1 5.249 2.115 14.551 0.00 0.00 H
ATOM 271 O X 1 4.492 10.374 6.877 0.00 0.00 O
ATOM 272 H X 1 3.735 9.896 7.215 0.00 0.00 H
ATOM 273 H X 1 5.249 9.896 7.215 0.00 0.00 H
ATOM 274 O X 1 4.492 10.374 14.213 0.00 0.00 O
ATOM 275 H X 1 3.735 9.896 14.551 0.00 0.00 H
ATOM 276 H X 1 5.249 9.896 14.551 0.00 0.00 H
ATOM 277 O X 1 8.984 2.593 6.877 0.00 0.00 O
ATOM 278 H X 1 8.228 2.115 7.215 0.00 0.00 H
ATOM 279 H X 1 9.741 2.115 7.215 0.00 0.00 H
ATOM 280 O X 1 8.984 2.593 14.213 0.00 0.00 O
ATOM 281 H X 1 8.228 2.115 14.551 0.00 0.00 H
ATOM 282 H X 1 9.741 2.115 14.551 0.00 0.00 H
ATOM 283 O X 1 8.984 10.374 6.877 0.00 0.00 O
ATOM 284 H X 1 8.228 9.896 7.215 0.00 0.00 H
ATOM 285 H X 1 9.741 9.896 7.215 0.00 0.00 H
ATOM 286 O X 1 8.984 10.374 14.213 0.00 0.00 O
ATOM 287 H X 1 8.228 9.896 14.551 0.00 0.00 H
ATOM 288 H X 1 9.741 9.896 14.551 0.00 0.00 H
END
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
...
# es: ENVIRONMENTSIMILARITY ...
es_cmatThe DISTANCE_MATRIX action with label es_cmat calculates the following quantities:| Quantity | Type | Description |
| es_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| es_cmat.x | matrix | the projection of the bond on the x axis |
| es_cmat.y | matrix | the projection of the bond on the y axis |
| es_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=1-384 CUTOFF ignore distances that have a value larger than this cutoff=0.425131
es_grpThe GROUP action with label es_grp calculates the following quantities:| Quantity | Type | Description |
| es_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=1-384
es_ones_OThe CONSTANT action with label es_ones_O calculates the following quantities:| Quantity | Type | Description |
| es_ones_O | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0
es_ones_HThe CONSTANT action with label es_ones_H calculates the following quantities:| Quantity | Type | Description |
| es_ones_H | vector | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1
es_O_matenv1The CUSTOM action with label es_O_matenv1 calculates the following quantities:| Quantity | Type | Description |
| es_O_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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(0.425131-w)/4)*(exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^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--0.0917)^2)/(4*0.0025))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.0025)))
es_O_env1The MATRIX_VECTOR_PRODUCT action with label es_O_env1 calculates the following quantities:| Quantity | Type | Description |
| es_O_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=es_O_matenv1,es_ones_O
es_H_matenv1The CUSTOM action with label es_H_matenv1 calculates the following quantities:| Quantity | Type | Description |
| es_H_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=es_cmat.x,es_cmat.y,es_cmat.z,es_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=0
es_H_env1The MATRIX_VECTOR_PRODUCT action with label es_H_env1 calculates the following quantities:| Quantity | Type | Description |
| es_H_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=es_H_matenv1,es_ones_H
esThe COMBINE action with label es calculates the following quantities:| Quantity | Type | Description |
| es | 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 ARGthe values input to this function=es_O_env1,es_H_env1
es_mtThe MORE_THAN action with label es_mt calculates the following quantities:| Quantity | Type | Description |
| es_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=es SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.5 NN=12 MM=24}
es_morethanThe SUM action with label es_morethan calculates the following quantities:| Quantity | Type | Description |
| es_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=es_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
es_meanThe MEAN action with label es_mean calculates the following quantities:| Quantity | Type | Description |
| es_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=es PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
In this case, all atoms are used as centers, but only neighbors of type O are taken into account.
References
More information about how this action can be used is available in the following articles:
- P. M. Piaggi, M. Parrinello, Calculation of phase diagrams in the multithermal-multibaric ensemble. The Journal of Chemical Physics. 150 (2019)
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword |
Type |
Default |
Description |
| SPECIES |
input |
none |
this keyword is used for colvars such as coordination number |
| SPECIESA |
input |
none |
this keyword is used for colvars such as the coordination number |
| SPECIESB |
input |
none |
this keyword is used for colvars such as the coordination number |
| CRYSTAL_STRUCTURE |
compulsory |
FCC |
Targeted crystal structure |
| LATTICE_CONSTANTS |
compulsory |
none |
Lattice constants |
| SIGMA |
compulsory |
0.1 |
the width to use for the gaussian kernels |
| LCUTOFF |
compulsory |
0.0001 |
any atoms separated by less than this tolerance should be ignored |
| LAMBDA |
compulsory |
100 |
Lambda parameter |
| CUTOFF |
compulsory |
3 |
how many multiples of sigma would you like to consider beyond the maximum distance in the environment |
| REFERENCE |
optional |
not used |
PDB files with relative distances from central atom |
| REFERENCE_ |
optional |
not used |
PDB files with relative distances from central atom |
| ATOM_NAMES_FILE |
optional |
not used |
PDB file with atom names for all atoms in SPECIES |
| LESS_THAN |
optional |
not used |
calculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN. |
| MORE_THAN |
optional |
not used |
calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN. |
| ALT_MIN |
optional |
not used |
calculate the minimum value |
| MIN |
optional |
not used |
calculate the minimum value |
| MAX |
optional |
not used |
calculate the maximum value |
| BETWEEN |
optional |
not used |
calculate the number of values that are within a certain range. Options for this keyword are explained in the documentation for BETWEEN. |
| HIGHEST |
optional |
false |
this flag allows you to recover the highest of these variables |
| HISTOGRAM |
optional |
not used |
calculate a discretized histogram of the distribution of values |
| LOWEST |
optional |
false |
this flag allows you to recover the lowest of these variables |
| SUM |
optional |
false |
calculate the sum of all the quantities |
| MEAN |
optional |
false |
calculate the mean of all the quantities |
