Project ID: plumID:25.005
Source: monomer_dimer/plumed.dat
Originally used with PLUMED version: 2.8.2
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 LENGTHthe units of lengths=A ENERGYthe units of energy=kcal/mol TIMEthe units of time=fs
The UNITS action with label calculates somethingFLUSHThis 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=1
OsolThe GROUP action with label Osol calculates the following quantities:| Quantity | Type | Description |
| Osol | 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=17-732:6
HsolThe GROUP action with label Hsol calculates the following quantities:| Quantity | Type | Description |
| Hsol | 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=18-732:6
c_boxThe FIXEDATOM action with label c_box calculates the following quantities:| Quantity | Type | Description |
| c_box | atoms | virtual atom calculated by FIXEDATOM action |
: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=11.075,10.526,10.622
c_box: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=11.075,10.526,10.622 SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
cn_ag_agThe COORDINATION action with label cn_ag_ag calculates the following quantities:| Quantity | Type | Description |
| cn_ag_ag | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
cn_ag_ag: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8 D_0 The d_0 parameter of the switching function=0.0
cn_ag_n1The COORDINATION action with label cn_ag_n1 calculates the following quantities:| Quantity | Type | Description |
| cn_ag_n1 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=6 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
cn_ag_n1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=6 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8 D_0 The d_0 parameter of the switching function=0.0
cn_ag_n2The COORDINATION action with label cn_ag_n2 calculates the following quantities:| Quantity | Type | Description |
| cn_ag_n2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8
cn_ag_n2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5 R_0The r_0 parameter of the switching function=3.25 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=8 D_0 The d_0 parameter of the switching function=0.0
cnThe COORDINATION action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=c_box GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Osol R_0The r_0 parameter of the switching function=2.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
cn: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=c_box GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=Osol R_0The r_0 parameter of the switching function=2.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
s1The COMBINE action with label s1 calculates the following quantities:| Quantity | Type | Description |
| s1 | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cn_ag_ag,cn_ag_n1,cn_ag_n2 COEFFICIENTS the coefficients of the arguments in your function=1,1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
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=s1,cn PACEthe frequency for hill addition=100 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=300 BIASFACTORuse well tempered metadynamics and use this bias factor=25 SIGMAthe widths of the Gaussian hills=0.05,0.01 HEIGHTthe heights of the Gaussian hills=3
cn_CH3The COORDINATIONNUMBER action with label cn_CH3 calculates the following quantities:| Quantity | Type | Description |
| cn_CH3 | vector | the coordination numbers of the specified atoms |
| cn_CH3_lowest | scalar | the smallest of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=13-732:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=14-732:6,15-732:6,16-732:6 R_0The r_0 parameter of the switching function=1.5 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
cn_CH3: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=13-732:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=14-732:6,15-732:6,16-732:6 R_0The r_0 parameter of the switching function=1.5 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn_CH3: COORDINATIONNUMBER SPECIESA=13-732:6 SPECIESB=14-732:6,15-732:6,16-732:6 R_0=1.5 LOWEST LOWMEM
cn_CH3_grpThe GROUP action with label cn_CH3_grp calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_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=13-732:6
cn_CH3_matThe CONTACT_MATRIX action with label cn_CH3_mat calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_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=13-732:6 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=14-732:6,15-732:6,16-732:6 R_0The r_0 parameter of the switching function=1.5 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_CH3_onesThe CONSTANT action with label cn_CH3_ones calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_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=360
cn_CH3The MATRIX_VECTOR_PRODUCT action with label cn_CH3 calculates the following quantities:| Quantity | Type | Description |
| cn_CH3 | 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=cn_CH3_mat,cn_CH3_ones
cn_CH3_caverageThe MEAN action with label cn_CH3_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_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=cn_CH3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_CH3_lowestThe LOWEST action with label cn_CH3_lowest calculates the following quantities:| Quantity | Type | Description |
| cn_CH3_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cn_CH3
# --- End of included input --- cn_COThe COORDINATIONNUMBER action with label cn_CO calculates the following quantities:| Quantity | Type | Description |
| cn_CO | vector | the coordination numbers of the specified atoms |
| cn_CO_lowest | scalar | the smallest of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=13-732:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=17-732:6 R_0The r_0 parameter of the switching function=1.5 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
cn_CO: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=13-732:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=17-732:6 R_0The r_0 parameter of the switching function=1.5 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn_CO: COORDINATIONNUMBER SPECIESA=13-732:6 SPECIESB=17-732:6 R_0=1.5 LOWEST LOWMEM
cn_CO_grpThe GROUP action with label cn_CO_grp calculates the following quantities:| Quantity | Type | Description |
| cn_CO_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=13-732:6
cn_CO_matThe CONTACT_MATRIX action with label cn_CO_mat calculates the following quantities:| Quantity | Type | Description |
| cn_CO_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=13-732:6 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=17-732:6 R_0The r_0 parameter of the switching function=1.5 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_CO_onesThe CONSTANT action with label cn_CO_ones calculates the following quantities:| Quantity | Type | Description |
| cn_CO_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=120
cn_COThe MATRIX_VECTOR_PRODUCT action with label cn_CO calculates the following quantities:| Quantity | Type | Description |
| cn_CO | 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=cn_CO_mat,cn_CO_ones
cn_CO_caverageThe MEAN action with label cn_CO_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_CO_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=cn_CO PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_CO_lowestThe LOWEST action with label cn_CO_lowest calculates the following quantities:| Quantity | Type | Description |
| cn_CO_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cn_CO
# --- End of included input --- cn_OHThe COORDINATIONNUMBER action with label cn_OH calculates the following quantities:| Quantity | Type | Description |
| cn_OH | vector | the coordination numbers of the specified atoms |
| cn_OH_lowest | scalar | the smallest of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=41-726:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=42-726:6 R_0The r_0 parameter of the switching function=1.4 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
cn_OH: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=41-726:6 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=42-726:6 R_0The r_0 parameter of the switching function=1.4 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn_OH: COORDINATIONNUMBER SPECIESA=41-726:6 SPECIESB=42-726:6 R_0=1.4 LOWEST LOWMEM
cn_OH_grpThe GROUP action with label cn_OH_grp calculates the following quantities:| Quantity | Type | Description |
| cn_OH_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=41-726:6
cn_OH_matThe CONTACT_MATRIX action with label cn_OH_mat calculates the following quantities:| Quantity | Type | Description |
| cn_OH_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=41-726:6 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=42-726:6 R_0The r_0 parameter of the switching function=1.4 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_OH_onesThe CONSTANT action with label cn_OH_ones calculates the following quantities:| Quantity | Type | Description |
| cn_OH_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=115
cn_OHThe MATRIX_VECTOR_PRODUCT action with label cn_OH calculates the following quantities:| Quantity | Type | Description |
| cn_OH | 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=cn_OH_mat,cn_OH_ones
cn_OH_caverageThe MEAN action with label cn_OH_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_OH_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=cn_OH PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_OH_lowestThe LOWEST action with label cn_OH_lowest calculates the following quantities:| Quantity | Type | Description |
| cn_OH_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cn_OH
# --- End of included input ---
HgrpThe GROUP action with label Hgrp calculates the following quantities:| Quantity | Type | Description |
| Hgrp | 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=9-12,14-732:6,15-732:6,16-732:6,18-732:6
cn_HThe COORDINATIONNUMBER action with label cn_H calculates the following quantities:| Quantity | Type | Description |
| cn_H | vector | the coordination numbers of the specified atoms |
| cn_H_lowest | scalar | the smallest of the colvars |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=Hgrp SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-732 R_0The r_0 parameter of the switching function=1.2 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility
cn_H: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=Hgrp SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1-732 R_0The r_0 parameter of the switching function=1.2 LOWEST this flag allows you to recover the lowest of these variables LOWMEM this flag does nothing and is present only to ensure back-compatibility D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# cn_H: COORDINATIONNUMBER SPECIESA=Hgrp SPECIESB=1-732 R_0=1.2 LOWEST LOWMEM
cn_H_grpThe GROUP action with label cn_H_grp calculates the following quantities:| Quantity | Type | Description |
| cn_H_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=Hgrp
cn_H_matThe CONTACT_MATRIX action with label cn_H_mat calculates the following quantities:| Quantity | Type | Description |
| cn_H_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=Hgrp 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=1-732 R_0The r_0 parameter of the switching function=1.2 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_H_onesThe CONSTANT action with label cn_H_ones calculates the following quantities:| Quantity | Type | Description |
| cn_H_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=732
cn_HThe MATRIX_VECTOR_PRODUCT action with label cn_H calculates the following quantities:| Quantity | Type | Description |
| cn_H | 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=cn_H_mat,cn_H_ones
cn_H_caverageThe MEAN action with label cn_H_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_H_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=cn_H PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_H_lowestThe LOWEST action with label cn_H_lowest calculates the following quantities:| Quantity | Type | Description |
| cn_H_lowest | scalar | the smallest element in the input vector if one vector specified. If multiple vectors of the same size specified the largest elements of these vector computed elementwise. |
: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=cn_H
# --- End of included input --- dHHThe DISTANCES action with label dHH calculates the following quantities:| Quantity | Type | Description |
| dHH | vector | the DISTANCES between the each pair of atoms that were specified |
| dHH_min | scalar | the minimum colvar |
: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Hgrp GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=Hgrp MINcalculate the minimum value={BETA=20} NOPBC ignore the periodic boundary conditions when calculating distances
# dHH: DISTANCES GROUPA=Hgrp GROUPB=Hgrp MIN={BETA=20} NOPBC
dHHThe DISTANCE action with label dHH calculates the following quantities:| Quantity | Type | Description |
| dHH | vector | the DISTANCE for each set of specified atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the pair of atom that we are calculating the distance between=9,9 ATOMS2the pair of atom that we are calculating the distance between=9,10 ATOMS3the pair of atom that we are calculating the distance between=9,11 ATOMS4the pair of atom that we are calculating the distance between=9,12 ATOMS5the pair of atom that we are calculating the distance between=9,14
dHH_me_minThe CUSTOM action with label dHH_me_min calculates the following quantities:| Quantity | Type | Description |
| dHH_me_min | 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=dHH FUNCthe function you wish to evaluate=exp(20/x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dHH_mec_minThe SUM action with label dHH_mec_min calculates the following quantities:| Quantity | Type | Description |
| dHH_mec_min | 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=dHH_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dHH_minThe CUSTOM action with label dHH_min calculates the following quantities:| Quantity | Type | Description |
| dHH_min | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dHH_mec_min FUNCthe function you wish to evaluate=20/log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
cThe COM action with label c calculates the following quantities:| Quantity | Type | Description |
| c | atoms | virtual atom calculated by COM action |
: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,2
dThe DISTANCE action with label d calculates the following quantities:| Quantity | Type | Description |
| d | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c,c_box
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,1
d2The DISTANCE action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,2
d3The DISTANCE action with label d3 calculates the following quantities:| Quantity | Type | Description |
| d3 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,3
d4The DISTANCE action with label d4 calculates the following quantities:| Quantity | Type | Description |
| d4 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,4
d5The DISTANCE action with label d5 calculates the following quantities:| Quantity | Type | Description |
| d5 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,5
d6The DISTANCE action with label d6 calculates the following quantities:| Quantity | Type | Description |
| d6 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c_box,6
a1The ANGLE action with label a1 calculates the following quantities:| Quantity | Type | Description |
| a1 | scalar | the ANGLE involving these atoms |
: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=3,1,6
a2The ANGLE action with label a2 calculates the following quantities:| Quantity | Type | Description |
| a2 | scalar | the ANGLE involving these atoms |
: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=4,2,5
dags1The DISTANCE action with label dags1 calculates the following quantities:| Quantity | Type | Description |
| dags1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,4
dags2The DISTANCE action with label dags2 calculates the following quantities:| Quantity | Type | Description |
| dags2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3
dsc1The DISTANCE action with label dsc1 calculates the following quantities:| Quantity | Type | Description |
| dsc1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,7
dsc2The DISTANCE action with label dsc2 calculates the following quantities:| Quantity | Type | Description |
| dsc2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,8
dnh1The DISTANCE action with label dnh1 calculates the following quantities:| Quantity | Type | Description |
| dnh1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9
dnh2The DISTANCE action with label dnh2 calculates the following quantities:| Quantity | Type | Description |
| dnh2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,12
cn_wallThe LOWER_WALLS action with label cn_wall calculates the following quantities:| Quantity | Type | Description |
| cn_wall.bias | scalar | the instantaneous value of the bias potential |
| cn_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=cn_CH3.lowest,cn_CO.lowest ATthe positions of the wall=2.55,0.47 KAPPAthe force constant for the wall=100,100
a_wallThe LOWER_WALLS action with label a_wall calculates the following quantities:| Quantity | Type | Description |
| a_wall.bias | scalar | the instantaneous value of the bias potential |
| a_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=a1,a2 ATthe positions of the wall=2.5,2.5 KAPPAthe force constant for the wall=100,100
d_wallThe UPPER_WALLS action with label d_wall calculates the following quantities:| Quantity | Type | Description |
| d_wall.bias | scalar | the instantaneous value of the bias potential |
| d_wall.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=d1,d2,d3,d4,d5,d6,dags1,dags2,dsc1,dsc2,dnh1,dnh2 ATthe positions of the wall=5,5,5,5,5,5,2.75,2.75,1.95,1.95,1.1,1.1 KAPPAthe force constant for the wall=100,100,100,100,100,100,100,100,100,100,100,100
resThe RESTRAINT action with label res calculates the following quantities:| Quantity | Type | Description |
| res.bias | scalar | the instantaneous value of the bias potential |
| res.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=d ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100
res: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=d ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=colvar ARGthe labels of the values that you would like to print to the file=*
