Project ID: plumID:19.051
Source: plumed.dat
Originally used with PLUMED version: not specified
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label calculates somethingcellThe CELL action with label cell calculates the following quantities: Quantity | Type | Description |
cell.ax | scalar | the ax component of the cell matrix |
cell.ay | scalar | the ay component of the cell matrix |
cell.az | scalar | the az component of the cell matrix |
cell.bx | scalar | the bx component of the cell matrix |
cell.by | scalar | the by component of the cell matrix |
cell.bz | scalar | the bz component of the cell matrix |
cell.cx | scalar | the cx component of the cell matrix |
cell.cy | scalar | the cy component of the cell matrix |
cell.cz | scalar | the cz component of the cell matrix |
: CELLGet the components of the simulation cell More details
cubThe FCCUBIC action with label cub calculates the following quantities: Quantity | Type | Description |
cub | vector | the symmetry function for each of the specified atoms |
cub_morethan | scalar | the number of colvars that have a value more than a threshold |
cub_mean | scalar | the mean of the colvars |
: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
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.={SMAP R_0=0.45 D_0=0.0 A=8 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-1.5708 THETA The Euler rotational angle theta=-0.61548 PSI The Euler rotational angle psi=0.785389
...
# cub: FCCUBIC ...
cub_grpThe GROUP action with label cub_grp calculates the following quantities: Quantity | Type | Description |
cub_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=1-1152
cub_matThe CONTACT_MATRIX action with label cub_mat calculates the following quantities: Quantity | Type | Description |
cub_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
cub_mat.x | matrix | the projection of the bond on the x axis |
cub_mat.y | matrix | the projection of the bond on the y axis |
cub_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-1152 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5} COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix
cub_xrotThe CUSTOM action with label cub_xrot calculates the following quantities: Quantity | Type | Description |
cub_xrot | 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=cub_mat.x,cub_mat.y,cub_mat.z FUNCthe function you wish to evaluate=0.577342*x+-0.707115*y+-0.408245*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub_yrotThe CUSTOM action with label cub_yrot calculates the following quantities: Quantity | Type | Description |
cub_yrot | 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=cub_mat.x,cub_mat.y,cub_mat.z FUNCthe function you wish to evaluate=0.577358*x+0.707098*y+-0.408252*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub_zrotThe CUSTOM action with label cub_zrot calculates the following quantities: Quantity | Type | Description |
cub_zrot | 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=cub_mat.x,cub_mat.y,cub_mat.z FUNCthe function you wish to evaluate=0.577351*x+-2.12073e-06*y+0.816496*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub_vfuncThe FCCUBIC_FUNC action with label cub_vfunc calculates the following quantities: Quantity | Type | Description |
cub_vfunc | matrix | the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix |
: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=cub_mat.x,cub_mat.y,cub_mat.z ALPHA The alpha parameter of the angular function=27
cub_wvfuncThe CUSTOM action with label cub_wvfunc calculates the following quantities: Quantity | Type | Description |
cub_wvfunc | 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=cub_vfunc,cub_mat.w 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
cub_onesThe CONSTANT action with label cub_ones calculates the following quantities: Quantity | Type | Description |
cub_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=1152
cubThe MATRIX_VECTOR_PRODUCT action with label cub calculates the following quantities: Quantity | Type | Description |
cub | 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=cub_wvfunc,cub_ones
cub_denomThe MATRIX_VECTOR_PRODUCT action with label cub_denom calculates the following quantities: Quantity | Type | Description |
cub_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cub_mat.w,cub_ones
cub_nThe CUSTOM action with label cub_n calculates the following quantities: Quantity | Type | Description |
cub_n | 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=cub,cub_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub_mtThe MORE_THAN action with label cub_mt calculates the following quantities: Quantity | Type | Description |
cub_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=cub_n SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.45 D_0=0.0 A=8 B=8}
cub_morethanThe SUM action with label cub_morethan calculates the following quantities: Quantity | Type | Description |
cub_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=cub_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub_meanThe MEAN action with label cub_mean calculates the following quantities: Quantity | Type | Description |
cub_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=cub_n PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
cub2The FCCUBIC action with label cub2 calculates the following quantities: Quantity | Type | Description |
cub2 | vector | the symmetry function for each of the specified atoms |
cub2_morethan | scalar | the number of colvars that have a value more than a threshold |
: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
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.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-1.5708 THETA The Euler rotational angle theta=0.61548 PSI The Euler rotational angle psi=2.35619
...
# cub2: FCCUBIC ...
cub2_grpThe GROUP action with label cub2_grp calculates the following quantities: Quantity | Type | Description |
cub2_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=1-1152
cub2_matThe CONTACT_MATRIX action with label cub2_mat calculates the following quantities: Quantity | Type | Description |
cub2_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
cub2_mat.x | matrix | the projection of the bond on the x axis |
cub2_mat.y | matrix | the projection of the bond on the y axis |
cub2_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-1152 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5} COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix
cub2_xrotThe CUSTOM action with label cub2_xrot calculates the following quantities: Quantity | Type | Description |
cub2_xrot | 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=cub2_mat.x,cub2_mat.y,cub2_mat.z FUNCthe function you wish to evaluate=0.577355*x+0.707101*y+0.40825*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub2_yrotThe CUSTOM action with label cub2_yrot calculates the following quantities: Quantity | Type | Description |
cub2_yrot | 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=cub2_mat.x,cub2_mat.y,cub2_mat.z FUNCthe function you wish to evaluate=-0.577345*x+0.707112*y+-0.408247*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub2_zrotThe CUSTOM action with label cub2_zrot calculates the following quantities: Quantity | Type | Description |
cub2_zrot | 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=cub2_mat.x,cub2_mat.y,cub2_mat.z FUNCthe function you wish to evaluate=-0.577351*x+2.12073e-06*y+0.816496*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub2_vfuncThe FCCUBIC_FUNC action with label cub2_vfunc calculates the following quantities: Quantity | Type | Description |
cub2_vfunc | matrix | the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix |
: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=cub2_mat.x,cub2_mat.y,cub2_mat.z ALPHA The alpha parameter of the angular function=27
cub2_wvfuncThe CUSTOM action with label cub2_wvfunc calculates the following quantities: Quantity | Type | Description |
cub2_wvfunc | 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=cub2_vfunc,cub2_mat.w 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
cub2_onesThe CONSTANT action with label cub2_ones calculates the following quantities: Quantity | Type | Description |
cub2_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=1152
cub2The MATRIX_VECTOR_PRODUCT action with label cub2 calculates the following quantities: Quantity | Type | Description |
cub2 | 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=cub2_wvfunc,cub2_ones
cub2_denomThe MATRIX_VECTOR_PRODUCT action with label cub2_denom calculates the following quantities: Quantity | Type | Description |
cub2_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cub2_mat.w,cub2_ones
cub2_nThe CUSTOM action with label cub2_n calculates the following quantities: Quantity | Type | Description |
cub2_n | 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=cub2,cub2_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub2_mtThe MORE_THAN action with label cub2_mt calculates the following quantities: Quantity | Type | Description |
cub2_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=cub2_n SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
cub2_morethanThe SUM action with label cub2_morethan calculates the following quantities: Quantity | Type | Description |
cub2_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=cub2_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cub3The FCCUBIC action with label cub3 calculates the following quantities: Quantity | Type | Description |
cub3 | vector | the symmetry function for each of the specified atoms |
cub3_morethan | scalar | the number of colvars that have a value more than a threshold |
: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
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.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=1.5708 THETA The Euler rotational angle theta=-1.29515 PSI The Euler rotational angle psi=0.785389
...
# cub3: FCCUBIC ...
cub3_grpThe GROUP action with label cub3_grp calculates the following quantities: Quantity | Type | Description |
cub3_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=1-1152
cub3_matThe CONTACT_MATRIX action with label cub3_mat calculates the following quantities: Quantity | Type | Description |
cub3_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
cub3_mat.x | matrix | the projection of the bond on the x axis |
cub3_mat.y | matrix | the projection of the bond on the y axis |
cub3_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-1152 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5} COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix
cub3_xrotThe CUSTOM action with label cub3_xrot calculates the following quantities: Quantity | Type | Description |
cub3_xrot | 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=cub3_mat.x,cub3_mat.y,cub3_mat.z FUNCthe function you wish to evaluate=-0.192453*x+0.707113*y+-0.680407*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub3_yrotThe CUSTOM action with label cub3_yrot calculates the following quantities: Quantity | Type | Description |
cub3_yrot | 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=cub3_mat.x,cub3_mat.y,cub3_mat.z FUNCthe function you wish to evaluate=-0.192452*x+-0.707101*y+-0.680419*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub3_zrotThe CUSTOM action with label cub3_zrot calculates the following quantities: Quantity | Type | Description |
cub3_zrot | 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=cub3_mat.x,cub3_mat.y,cub3_mat.z FUNCthe function you wish to evaluate=-0.962249*x+-3.53454e-06*y+0.272169*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub3_vfuncThe FCCUBIC_FUNC action with label cub3_vfunc calculates the following quantities: Quantity | Type | Description |
cub3_vfunc | matrix | the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix |
: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=cub3_mat.x,cub3_mat.y,cub3_mat.z ALPHA The alpha parameter of the angular function=27
cub3_wvfuncThe CUSTOM action with label cub3_wvfunc calculates the following quantities: Quantity | Type | Description |
cub3_wvfunc | 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=cub3_vfunc,cub3_mat.w 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
cub3_onesThe CONSTANT action with label cub3_ones calculates the following quantities: Quantity | Type | Description |
cub3_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=1152
cub3The MATRIX_VECTOR_PRODUCT action with label cub3 calculates the following quantities: Quantity | Type | Description |
cub3 | 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=cub3_wvfunc,cub3_ones
cub3_denomThe MATRIX_VECTOR_PRODUCT action with label cub3_denom calculates the following quantities: Quantity | Type | Description |
cub3_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cub3_mat.w,cub3_ones
cub3_nThe CUSTOM action with label cub3_n calculates the following quantities: Quantity | Type | Description |
cub3_n | 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=cub3,cub3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub3_mtThe MORE_THAN action with label cub3_mt calculates the following quantities: Quantity | Type | Description |
cub3_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=cub3_n SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
cub3_morethanThe SUM action with label cub3_morethan calculates the following quantities: Quantity | Type | Description |
cub3_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=cub3_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cub4The FCCUBIC action with label cub4 calculates the following quantities: Quantity | Type | Description |
cub4 | vector | the symmetry function for each of the specified atoms |
cub4_morethan | scalar | the number of colvars that have a value more than a threshold |
: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
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.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-0.2014 THETA The Euler rotational angle theta=1.84644 PSI The Euler rotational angle psi=1.71269
...
# cub4: FCCUBIC ...
cub4_grpThe GROUP action with label cub4_grp calculates the following quantities: Quantity | Type | Description |
cub4_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=1-1152
cub4_matThe CONTACT_MATRIX action with label cub4_mat calculates the following quantities: Quantity | Type | Description |
cub4_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
cub4_mat.x | matrix | the projection of the bond on the x axis |
cub4_mat.y | matrix | the projection of the bond on the y axis |
cub4_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-1152 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5} COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix
cub4_xrotThe CUSTOM action with label cub4_xrot calculates the following quantities: Quantity | Type | Description |
cub4_xrot | 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=cub4_mat.x,cub4_mat.y,cub4_mat.z FUNCthe function you wish to evaluate=-0.192457*x+-0.235696*y+0.95258*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub4_yrotThe CUSTOM action with label cub4_yrot calculates the following quantities: Quantity | Type | Description |
cub4_yrot | 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=cub4_mat.x,cub4_mat.y,cub4_mat.z FUNCthe function you wish to evaluate=-0.962241*x+0.235742*y+-0.13608*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub4_zrotThe CUSTOM action with label cub4_zrot calculates the following quantities: Quantity | Type | Description |
cub4_zrot | 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=cub4_mat.x,cub4_mat.y,cub4_mat.z FUNCthe function you wish to evaluate=-0.19249*x+-0.942801*y+-0.272166*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub4_vfuncThe FCCUBIC_FUNC action with label cub4_vfunc calculates the following quantities: Quantity | Type | Description |
cub4_vfunc | matrix | the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix |
: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=cub4_mat.x,cub4_mat.y,cub4_mat.z ALPHA The alpha parameter of the angular function=27
cub4_wvfuncThe CUSTOM action with label cub4_wvfunc calculates the following quantities: Quantity | Type | Description |
cub4_wvfunc | 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=cub4_vfunc,cub4_mat.w 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
cub4_onesThe CONSTANT action with label cub4_ones calculates the following quantities: Quantity | Type | Description |
cub4_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=1152
cub4The MATRIX_VECTOR_PRODUCT action with label cub4 calculates the following quantities: Quantity | Type | Description |
cub4 | 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=cub4_wvfunc,cub4_ones
cub4_denomThe MATRIX_VECTOR_PRODUCT action with label cub4_denom calculates the following quantities: Quantity | Type | Description |
cub4_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cub4_mat.w,cub4_ones
cub4_nThe CUSTOM action with label cub4_n calculates the following quantities: Quantity | Type | Description |
cub4_n | 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=cub4,cub4_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub4_mtThe MORE_THAN action with label cub4_mt calculates the following quantities: Quantity | Type | Description |
cub4_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=cub4_n SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
cub4_morethanThe SUM action with label cub4_morethan calculates the following quantities: Quantity | Type | Description |
cub4_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=cub4_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cub5The FCCUBIC action with label cub5 calculates the following quantities: Quantity | Type | Description |
cub5 | vector | the symmetry function for each of the specified atoms |
cub5_morethan | scalar | the number of colvars that have a value more than a threshold |
: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. This action is a shortcut. More details ...
SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-1152 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5}
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.={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 PHI The Euler rotational angle phi=-0.61548 THETA The Euler rotational angle theta=-1.5708 PSI The Euler rotational angle psi=-0.785398
...
# cub5: FCCUBIC ...
cub5_grpThe GROUP action with label cub5_grp calculates the following quantities: Quantity | Type | Description |
cub5_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=1-1152
cub5_matThe CONTACT_MATRIX action with label cub5_mat calculates the following quantities: Quantity | Type | Description |
cub5_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
cub5_mat.x | matrix | the projection of the bond on the x axis |
cub5_mat.y | matrix | the projection of the bond on the y axis |
cub5_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-1152 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5} COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix
cub5_xrotThe CUSTOM action with label cub5_xrot calculates the following quantities: Quantity | Type | Description |
cub5_xrot | 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=cub5_mat.x,cub5_mat.y,cub5_mat.z FUNCthe function you wish to evaluate=0.577352*x+-0.408246*y+0.707107*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub5_yrotThe CUSTOM action with label cub5_yrot calculates the following quantities: Quantity | Type | Description |
cub5_yrot | 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=cub5_mat.x,cub5_mat.y,cub5_mat.z FUNCthe function you wish to evaluate=0.577349*x+-0.408251*y+-0.707107*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub5_zrotThe CUSTOM action with label cub5_zrot calculates the following quantities: Quantity | Type | Description |
cub5_zrot | 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=cub5_mat.x,cub5_mat.y,cub5_mat.z FUNCthe function you wish to evaluate=0.577351*x+0.816496*y+-3.67321e-06*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub5_vfuncThe FCCUBIC_FUNC action with label cub5_vfunc calculates the following quantities: Quantity | Type | Description |
cub5_vfunc | matrix | the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix |
: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=cub5_mat.x,cub5_mat.y,cub5_mat.z ALPHA The alpha parameter of the angular function=27
cub5_wvfuncThe CUSTOM action with label cub5_wvfunc calculates the following quantities: Quantity | Type | Description |
cub5_wvfunc | 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=cub5_vfunc,cub5_mat.w 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
cub5_onesThe CONSTANT action with label cub5_ones calculates the following quantities: Quantity | Type | Description |
cub5_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=1152
cub5The MATRIX_VECTOR_PRODUCT action with label cub5 calculates the following quantities: Quantity | Type | Description |
cub5 | 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=cub5_wvfunc,cub5_ones
cub5_denomThe MATRIX_VECTOR_PRODUCT action with label cub5_denom calculates the following quantities: Quantity | Type | Description |
cub5_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cub5_mat.w,cub5_ones
cub5_nThe CUSTOM action with label cub5_n calculates the following quantities: Quantity | Type | Description |
cub5_n | 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=cub5,cub5_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub5_mtThe MORE_THAN action with label cub5_mt calculates the following quantities: Quantity | Type | Description |
cub5_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=cub5_n SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.05 D_0=0.4 A=16 B=8}
cub5_morethanThe SUM action with label cub5_morethan calculates the following quantities: Quantity | Type | Description |
cub5_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=cub5_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
centercubThe AROUND action with label centercub calculates the following quantities: Quantity | Type | Description |
centercub_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=cub ATOMan alternative to ORIGIN=1153 XLOWER the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=-1.2 XUPPER the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=1.2 SIGMAthe width of the function to be used for kernel density estimation=0.5 MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={SMAP R_0=0.5 D_0=0.0 A=8 B=8}
# centercub: AROUND DATA=cub ATOM=1153 XLOWER=-1.2 XUPPER=1.2 SIGMA=0.5 MORE_THAN={SMAP R_0=0.5 D_0=0.0 A=8 B=8}
centercub_grpThe GROUP action with label centercub_grp calculates the following quantities: Quantity | Type | Description |
centercub_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=cub
cub_centercub_mtThe MORE_THAN action with label cub_centercub_mt calculates the following quantities: Quantity | Type | Description |
cub_centercub_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=cub SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.5 D_0=0.0 A=8 B=8}
centercub_mtThe CUSTOM action with label centercub_mt calculates the following quantities: Quantity | Type | Description |
centercub_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=cub_centercub_mt,centercub 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
centercub_morethanThe SUM action with label centercub_morethan calculates the following quantities: Quantity | Type | Description |
centercub_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=centercub_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- sidecubThe AROUND action with label sidecub calculates the following quantities: Quantity | Type | Description |
sidecub_lessthan | scalar | the number of cvs in the region of interest that are less 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=cub ATOMan alternative to ORIGIN=1153 XLOWER the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=-2.3 XUPPER the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=2.3 SIGMAthe width of the function to be used for kernel density estimation=0.5 OUTSIDE calculate quantities for colvars that are on atoms outside the region of interest LESS_THANcalcualte the number of colvars that are inside the region of interest and that are less than a certain threshold={SMAP R_0=0.5 D_0=-0.1 A=8 B=2}
# sidecub: AROUND DATA=cub ATOM=1153 XLOWER=-2.3 XUPPER=2.3 SIGMA=0.5 OUTSIDE LESS_THAN={SMAP R_0=0.5 D_0=-0.1 A=8 B=2}
sidecub_grpThe GROUP action with label sidecub_grp calculates the following quantities: Quantity | Type | Description |
sidecub_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=cub
cub_sidecub_ltThe LESS_THAN action with label cub_sidecub_lt calculates the following quantities: Quantity | Type | Description |
cub_sidecub_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=cub SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.5 D_0=-0.1 A=8 B=2}
sidecub_ltThe CUSTOM action with label sidecub_lt calculates the following quantities: Quantity | Type | Description |
sidecub_lt | 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=cub_sidecub_lt,sidecub 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
sidecub_lessthanThe SUM action with label sidecub_lessthan calculates the following quantities: Quantity | Type | Description |
sidecub_lessthan | 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=sidecub_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- bordercubThe AROUND action with label bordercub calculates the following quantities: Quantity | Type | Description |
bordercub_lessthan | scalar | the number of cvs in the region of interest that are less 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=cub ATOMan alternative to ORIGIN=1153 XLOWER the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=-7.0 XUPPER the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)=7.0 SIGMAthe width of the function to be used for kernel density estimation=0.5 OUTSIDE calculate quantities for colvars that are on atoms outside the region of interest LESS_THANcalcualte the number of colvars that are inside the region of interest and that are less than a certain threshold={SMAP R_0=0.5 D_0=-0.45 A=8 B=8}
# bordercub: AROUND DATA=cub ATOM=1153 XLOWER=-7.0 XUPPER=7.0 SIGMA=0.5 OUTSIDE LESS_THAN={SMAP R_0=0.5 D_0=-0.45 A=8 B=8}
bordercub_grpThe GROUP action with label bordercub_grp calculates the following quantities: Quantity | Type | Description |
bordercub_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=cub
cub_bordercub_ltThe LESS_THAN action with label cub_bordercub_lt calculates the following quantities: Quantity | Type | Description |
cub_bordercub_lt | vector | the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors |
: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=cub SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.5 D_0=-0.45 A=8 B=8}
bordercub_ltThe CUSTOM action with label bordercub_lt calculates the following quantities: Quantity | Type | Description |
bordercub_lt | 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=cub_bordercub_lt,bordercub 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
bordercub_lessthanThe SUM action with label bordercub_lessthan calculates the following quantities: Quantity | Type | Description |
bordercub_lessthan | 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=bordercub_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
metadThe METAD action with label metad calculates the following quantities: Quantity | Type | Description |
metad.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=sidecub.lessthan
PACEthe frequency for hill addition=1600 HEIGHTthe heights of the Gaussian hills=0.15 SIGMAthe widths of the Gaussian hills=600 FILE a file in which the list of added hills is stored=HILLS
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=0.60 BIASFACTORuse well tempered metadynamics and use this bias factor=90
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=50 SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.1
...
wallThe LOWER_WALLS action with label wall calculates the following quantities: Quantity | Type | Description |
wall.bias | scalar | the instantaneous value of the bias potential |
wall.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=centercub.morethan ATthe positions of the wall=140 KAPPAthe force constant for the wall=2.0
notwin2The UPPER_WALLS action with label notwin2 calculates the following quantities: Quantity | Type | Description |
notwin2.bias | scalar | the instantaneous value of the bias potential |
notwin2.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=cub2.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.4
notwin3The UPPER_WALLS action with label notwin3 calculates the following quantities: Quantity | Type | Description |
notwin3.bias | scalar | the instantaneous value of the bias potential |
notwin3.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=cub3.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.2
notwin4The UPPER_WALLS action with label notwin4 calculates the following quantities: Quantity | Type | Description |
notwin4.bias | scalar | the instantaneous value of the bias potential |
notwin4.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=cub4.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.2
notwin5The UPPER_WALLS action with label notwin5 calculates the following quantities: Quantity | Type | Description |
notwin5.bias | scalar | the instantaneous value of the bias potential |
notwin5.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=cub5.morethan ATthe positions of the wall=14 KAPPAthe force constant for the wall=0.1
softliquidThe LOWER_WALLS action with label softliquid calculates the following quantities: Quantity | Type | Description |
softliquid.bias | scalar | the instantaneous value of the bias potential |
softliquid.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=bordercub.lessthan ATthe positions of the wall=30 KAPPAthe force constant for the wall=0.005
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cell.ax,cub.*,metad.bias,wall.bias,notwin2.bias,notwin3.bias,notwin4.bias,notwin5.bias,softliquid.bias FILEthe name of the file on which to output these quantities=FES
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cub2.*,cub3.*,cub4.*,cub5.*,centercub.*,sidecub.*,sidecub.*,bordercub.* FILEthe name of the file on which to output these quantities=COLVAR
ENDPLUMEDTerminate plumed input. More details