Project ID: plumID:23.028
Source: DeepMD_simulations/FES_calculation/plumed.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details.
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label calculates somethingHThe GROUP action with label H calculates the following quantities:| Quantity | Type | Description |
| H | 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=27,28,29,30,31,32,33,34,35,36,54,55,56,57,58,59,62,86,87,88,89,90,91,92,93,94,136,137,138,139,140,141,142,143,144,145,146,147,148,164,165,166,167,168,183,184,185,186,187,209,210,211,221,222,223,227,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,377,378,379,380,381,384,386,387,388,390,391,392
NThe GROUP action with label N calculates the following quantities:| Quantity | Type | Description |
| N | 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=17,18,19,20,21,22,23,24,25,26,48,49,50,51,52,53,61,77,78,79,80,81,82,83,84,85,123,124,125,126,127,128,129,130,131,132,133,134,135,159,160,161,162,163,178,179,180,181,182,206,207,208,218,219,220,226,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,372,373,374,375,376,383,385,389
LiThe GROUP action with label Li calculates the following quantities:| Quantity | Type | Description |
| Li | 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=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,37,38,39,40,41,42,43,44,45,46,47,60,63,64,65,66,67,68,69,70,71,72,73,74,75,76,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,149,150,151,152,153,154,155,156,157,158,169,170,171,172,173,174,175,176,177,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,212,213,214,215,216,217,224,225,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,362,363,364,365,366,367,368,369,370,371,382
eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
max_nn_fix11The COORDINATIONNUMBER action with label max_nn_fix11 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11 | vector | the coordination numbers of the specified atoms |
| max_nn_fix11_max | scalar | the maximum colvar |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=249 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=260 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.={RATIONAL R_0=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.01}
# max_nn_fix11: COORDINATIONNUMBER SPECIESA=249 SPECIESB=260 SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01}
max_nn_fix11_grpThe GROUP action with label max_nn_fix11_grp calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11_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=249
max_nn_fix11_matThe CONTACT_MATRIX action with label max_nn_fix11_mat calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=249 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=260 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.={RATIONAL R_0=1.6 D_MAX=5}
max_nn_fix11_onesThe CONSTANT action with label max_nn_fix11_ones calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11_ones | scalar | 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=1
max_nn_fix11The MATRIX_VECTOR_PRODUCT action with label max_nn_fix11 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11 | 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=max_nn_fix11_mat,max_nn_fix11_ones
max_nn_fix11_caverageThe MEAN action with label max_nn_fix11_caverage calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11_caverage | 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=max_nn_fix11 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix11_me_maxThe CUSTOM action with label max_nn_fix11_me_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11_me_max | 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=max_nn_fix11 FUNCthe function you wish to evaluate=exp(x/0.01) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix11_mec_maxThe SUM action with label max_nn_fix11_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11_mec_max | 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=max_nn_fix11_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix11_maxThe CUSTOM action with label max_nn_fix11_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix11_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_nn_fix11_mec_max FUNCthe function you wish to evaluate=0.01*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- max_nn_fix12The COORDINATIONNUMBER action with label max_nn_fix12 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12 | vector | the coordination numbers of the specified atoms |
| max_nn_fix12_max | scalar | the maximum colvar |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=249 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=261 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.={RATIONAL R_0=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.01}
# max_nn_fix12: COORDINATIONNUMBER SPECIESA=249 SPECIESB=261 SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01}
max_nn_fix12_grpThe GROUP action with label max_nn_fix12_grp calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12_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=249
max_nn_fix12_matThe CONTACT_MATRIX action with label max_nn_fix12_mat calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=249 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=261 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.={RATIONAL R_0=1.6 D_MAX=5}
max_nn_fix12_onesThe CONSTANT action with label max_nn_fix12_ones calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12_ones | scalar | 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=1
max_nn_fix12The MATRIX_VECTOR_PRODUCT action with label max_nn_fix12 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12 | 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=max_nn_fix12_mat,max_nn_fix12_ones
max_nn_fix12_caverageThe MEAN action with label max_nn_fix12_caverage calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12_caverage | 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=max_nn_fix12 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix12_me_maxThe CUSTOM action with label max_nn_fix12_me_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12_me_max | 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=max_nn_fix12 FUNCthe function you wish to evaluate=exp(x/0.01) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix12_mec_maxThe SUM action with label max_nn_fix12_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12_mec_max | 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=max_nn_fix12_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix12_maxThe CUSTOM action with label max_nn_fix12_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix12_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_nn_fix12_mec_max FUNCthe function you wish to evaluate=0.01*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- max_nn_fix22The COORDINATIONNUMBER action with label max_nn_fix22 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22 | vector | the coordination numbers of the specified atoms |
| max_nn_fix22_max | scalar | the maximum colvar |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=259 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=261 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.={RATIONAL R_0=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.01}
# max_nn_fix22: COORDINATIONNUMBER SPECIESA=259 SPECIESB=261 SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01}
max_nn_fix22_grpThe GROUP action with label max_nn_fix22_grp calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22_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=259
max_nn_fix22_matThe CONTACT_MATRIX action with label max_nn_fix22_mat calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=259 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=261 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.={RATIONAL R_0=1.6 D_MAX=5}
max_nn_fix22_onesThe CONSTANT action with label max_nn_fix22_ones calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22_ones | scalar | 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=1
max_nn_fix22The MATRIX_VECTOR_PRODUCT action with label max_nn_fix22 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22 | 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=max_nn_fix22_mat,max_nn_fix22_ones
max_nn_fix22_caverageThe MEAN action with label max_nn_fix22_caverage calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22_caverage | 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=max_nn_fix22 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix22_me_maxThe CUSTOM action with label max_nn_fix22_me_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22_me_max | 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=max_nn_fix22 FUNCthe function you wish to evaluate=exp(x/0.01) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix22_mec_maxThe SUM action with label max_nn_fix22_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22_mec_max | 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=max_nn_fix22_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix22_maxThe CUSTOM action with label max_nn_fix22_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix22_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_nn_fix22_mec_max FUNCthe function you wish to evaluate=0.01*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- max_nn_fix23The COORDINATIONNUMBER action with label max_nn_fix23 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23 | vector | the coordination numbers of the specified atoms |
| max_nn_fix23_max | scalar | the maximum colvar |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=261 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=342 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.={RATIONAL R_0=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.01}
# max_nn_fix23: COORDINATIONNUMBER SPECIESA=261 SPECIESB=342 SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01}
max_nn_fix23_grpThe GROUP action with label max_nn_fix23_grp calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23_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=261
max_nn_fix23_matThe CONTACT_MATRIX action with label max_nn_fix23_mat calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=261 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=342 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.={RATIONAL R_0=1.6 D_MAX=5}
max_nn_fix23_onesThe CONSTANT action with label max_nn_fix23_ones calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23_ones | scalar | 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=1
max_nn_fix23The MATRIX_VECTOR_PRODUCT action with label max_nn_fix23 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23 | 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=max_nn_fix23_mat,max_nn_fix23_ones
max_nn_fix23_caverageThe MEAN action with label max_nn_fix23_caverage calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23_caverage | 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=max_nn_fix23 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix23_me_maxThe CUSTOM action with label max_nn_fix23_me_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23_me_max | 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=max_nn_fix23 FUNCthe function you wish to evaluate=exp(x/0.01) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix23_mec_maxThe SUM action with label max_nn_fix23_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23_mec_max | 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=max_nn_fix23_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix23_maxThe CUSTOM action with label max_nn_fix23_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix23_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_nn_fix23_mec_max FUNCthe function you wish to evaluate=0.01*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- max_nn_fix33The COORDINATIONNUMBER action with label max_nn_fix33 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33 | vector | the coordination numbers of the specified atoms |
| max_nn_fix33_max | scalar | the maximum colvar |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=129 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=342 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.={RATIONAL R_0=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.01}
# max_nn_fix33: COORDINATIONNUMBER SPECIESA=129 SPECIESB=342 SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01}
max_nn_fix33_grpThe GROUP action with label max_nn_fix33_grp calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33_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=129
max_nn_fix33_matThe CONTACT_MATRIX action with label max_nn_fix33_mat calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=129 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=342 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.={RATIONAL R_0=1.6 D_MAX=5}
max_nn_fix33_onesThe CONSTANT action with label max_nn_fix33_ones calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33_ones | scalar | 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=1
max_nn_fix33The MATRIX_VECTOR_PRODUCT action with label max_nn_fix33 calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33 | 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=max_nn_fix33_mat,max_nn_fix33_ones
max_nn_fix33_caverageThe MEAN action with label max_nn_fix33_caverage calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33_caverage | 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=max_nn_fix33 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix33_me_maxThe CUSTOM action with label max_nn_fix33_me_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33_me_max | 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=max_nn_fix33 FUNCthe function you wish to evaluate=exp(x/0.01) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix33_mec_maxThe SUM action with label max_nn_fix33_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33_mec_max | 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=max_nn_fix33_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_fix33_maxThe CUSTOM action with label max_nn_fix33_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_fix33_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_nn_fix33_mec_max FUNCthe function you wish to evaluate=0.01*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes2The OPES_METAD action with label opes2 calculates the following quantities:| Quantity | Type | Description |
| opes2.bias | scalar | the instantaneous value of the bias potential |
| opes2.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes2.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes2.neff | scalar | effective sample size |
| opes2.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=max_nn_fix11.max
PACEthe frequency for kernel deposition=250
BARRIERthe free energy barrier to be overcome=220
TEMP temperature=750
FILE a file in which the list of all deposited kernels is stored=Kernels_Bb220.data.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=Restart.data
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State_Bb220.data
STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=2000
STORE_STATES append to STATE_WFILE instead of ovewriting it each time
... OPES_METAD
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes2
ARGthe labels of the scalars on which the bias will act=max_nn_fix11.max
PACEthe frequency for kernel deposition=250
BARRIERthe free energy barrier to be overcome=220
TEMP temperature=750
FILE a file in which the list of all deposited kernels is stored=Kernels_Bb220.data.data
STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=Restart.data
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State_Bb220.data
STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=2000
STORE_STATES append to STATE_WFILE instead of ovewriting it each time
SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=80
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=400
